It is because craft is a collective term and OED mentions that it might be originated as an elliptical expression. Craft itself is used as aircraft as well. OED includes the following explanation for the fifth definition of craft:
V. Applied to boats, ships, and fishing requisites.
These uses were probably colloquial with watermen, fishers, and seamen some time before they appeared in print, so that the history is not evidenced; but the expression is probably elliptical, sense 9 being = vessels of small craft, i.e. small trading vessels, or of small seaman's art, and sense 10 = requisites of the fisherman's craft. It is not impossible that the latter was the earlier: cf. quot. 1704 at sense 10. The want in English of any general collective term for all sorts of ‘vessels for water carriage’ naturally made craft a useful stop-gap.
a. collect. (const. as pl.) Vessels or boats.
(a) originally only in small craft n.
(b) Hence, without small, in same sense; later, in the general sense of vessels of all kinds for water carriage and transport.
b. (with a and pl.) A small vessel or boat; any sailing or floating vessel.
c. An aircraft or spacecraft.
10. collect. Implements used in catching or killing fish; in mod. use chiefly in Whale-fishery: see quot. 1887.
Craft, is a Sea word signifying all manner of Lines, Nets, Hooks, &c. which serve for Fishing; and because those that use the Fishing Trade use Small Vessels..they call all such little Vessels Small Craft.
1704 J. Harris Lexicon Technicum
The harpoons, hand-lances, and boat-spades, are usually called ‘craft’, and the other implements ‘gear’.
1887 G. B. Goode Fisheries U.S.: Hist. & Methods II. 241
However, OED mentions that the plural form aircrafts is rare and there is one citation that aircrafts is used:
His world-famed aircrafts.
1903 Aeronaut. Jrnl. 7 81/1
OED also adds that the word can be understood, esp. when used in the plural, to include other kinds of heavier-than-air machine, such as helicopters. The word is often preferred to aeroplane or airplane in official and military contexts:
Will you please make the following terminology effective in all British official correspondence: For ‘aeroplane’ the word ‘aircraft’ should be used.
1943 W. S. Churchill Telegram 15 June in Second World War (1952) V. 566