The traditional Golden Dawn attribution places the elemental tools as follows: Pentacle=Earth, Dagger=Air, Cup=Water, Wand=Fire. In several books on Ceremonial Magic, I have seen the attributions for the Dagger and Wand switched. This is often due, at least in my reading, to a lack of deep knowledge. Until recently, a lot of the books written about Ceremonial Magic (that weren't Crowley, Regardie, etc.) were obviously written by 'outsiders', i.e., people who do not actually practice Magic. (Some Magical people call them 'muggles'.)
Case in point: the book The Secrets of High Magic, by Francis Melville, gives these reversed attributions, but leaves the Tarot attributions (Wands=Fire, Swords=Air) intact. While I quite like this book - or at least, the older version of it - it was obviously not written by a practicing Magician.
I agree that the Wand would, on the surface, seem to be more Air-like. But the founders of the original Golden Dawn (and the early leaders of the offshoot groups, such as the Stella Matutina) knew what they were doing, and arranged the attributions to as to be almost perfectly symmetrical. The Wand is a (blatant) phallic symbol, which makes more sense when attributed to Fire; it perfectly compliments the receptive Cup, which is almost always attributed to Water. Both the symbolism and the elemental attributions line up perfectly.
Likewise, the Dagger's attribution to Air forms a perfect compliment to the attribution of the Pentacle to Earth. If the Wand and Cup can be thought of as the male and female sex organs, then the Dagger and Pentacle can be thought of as a sword and shield; seeing as how the Pentacle is primarily a defensive tool, this analogy serves reasonably well. (Although one should not think of the Dagger being a sword in a literal sense; more on this in a bit.)
Unfortunately, some people are not so easily convinced. One person I saw on a forum said that the attributions of the Pentacle, Cup, and Wand were all well and good, but felt that the Dagger was assigned to Air simply because that was all that was left. A miniature flame war broke out on the subject, but was quickly cooled down by a moderator. I agree that the Dagger's attribution is not so obvious, but there are a few things that make sense to me.
Donald Michael Kraig, in his book Modern Magick: Twelve Lessons in the High Magickal Arts, says that the Dagger can be thought of as the tip of a spear that is thrown through the air. Personally, my favorite explanation is given by the ubiquitous Aleister Crowley, in his Book 4:
The Sword or Dagger is attributed to air, all-wandering, all-penetrating, but unstable; not a phenomenon subtle like fire, not a chemical combination like water, but a mixture of gases.
One might say that the Pantacle is the bread of life, and the Sword the knife which cuts it up. One must have ideas, but one must criticize them.
- Book 4, Part II, Chapter VIII
(Note here that Crowley refers to the Sword; more on this in a bit.)
I think the biggest mistake people make in trying to make all the attributions 'fit' is assuming that there is only one dagger, one wand, et cetera. Even leaving aside the Lotus Wand, there are numerous wands/scepters that are used almost exclusively in initiation ceremonies, such as the Scepter of Power.
In many versions of the Lesser Ritual of the Pentagram, the Archangel Raphael is visualized as carrying a caduceus; since Raphael is associated with Air, this has served as another point for some to think of the Wand being attributed to Air. Likewise, the Archangel Michael - who is associated with Fire - is sometimes visualized in the LRP as holding a flaming sword.
This brings me to my second point: the confusion of the Dagger with the Sword. Strictly speaking, in a Golden Dawn context the Magical Sword is not an elemental weapon; it is associated with the 5th Sephira, Geburah. As the color of Geburah on the Queen Scale is scarlet, it makes sense for the Magical Sword to be painted this color on the hilt and pommel. As emerald green is the flashing color of scarlet, it therefore also makes practical sense to use this color to paint the various names onto the Magical Sword.
Unfortunately, these two colors - red with green lettering - are virtually identical to the primary colors of the Wand; the Wand being the tool associated with Fire. For someone who equates the Dagger with the Sword symbolically, this could be seen as supportive of their conception of Dagger=Fire. To me, this is not only confusing to an outsider, but I feel it would be somewhat distracting to someone practicing magic. I think this may be why the Wand is also painted with yellow parts, to reinforce its Fire-like appearance and distance it visually from the Magical Sword.
The solution to this would be to not consider the elemental tools from a strictly elemental viewpoint, unless such associations are directly relevant to the working at hand. In Book 4, Crowley's directions for making these tools tend to focus far more on the appropriate sizes and the materials to use, rather than coloration. (In fact, going by the book would leave most of the tools with no coloration except for that of the materials from which they were made.) Crowley also goes into great detail on the symbolism of the tools apart from their elemental associations; he goes on at length about the Sword representing the analytical faculty, the Wand representing one's will, etc.
Speaking of Crowley, why does he seem to equate the Dagger with the Sword? Well, it turns out there are two daggers, or a dagger and a sword if you will. The first Dagger is associated with the Scourge and Chain; these three tools represent the alchemical principles of Mercury, Sulfur, and Salt, respectively.
The second blade - one of the four elemental tools - is almost always referred to as the Sword, but it can certainly be a dagger:
Only the simple can withstand the sword. As we are below the Abyss, this weapon is then entirely destructive: it divides Satan against Satan. It is only in the lower forms of Magick, the purely human forms, that the Sword has become so important a weapon. A dagger should be sufficient.
But the mind of man is normally so important to him that the sword is actually the largest of his weapons; happy is he who can make the dagger suffice!
- Book 4, Part II, Chapter VIII
So in a Thelemic context, the tool associated with Air can be either a Dagger or a Sword; though it is assumed to be the latter here, Liber 412 refers to the tool as the Dagger.
For a while, I wondered why the traditional Golden Dawn version of the Tarot had the Swords as a suit if it would have been more correct to call it Daggers. Looking at the artwork on some Tarot decks, I think that the ultimate fact is this: the Dagger could in theory be extended into a Sword, so long as it was still obviously an Air tool. It doesn't matter if there are two swords or two daggers, so long as there isn't any confusion between the two tools. (I think this is the principle behind the use of a non-Air dagger in the LRP, but I haven't found out for sure.) For the Magical Sword, though, a full-length Sword would undoubtedly be the more correct association to Geburah.
In summary: one could have as many swords, daggers, and wands as one likes, so long as they are kept separate from one another symbolically, practically, and visually.