Hmmm, that's quite a good question. Well, the animators probably have the main characters using the hand seals (ex. Sasuke's fire techniques & Naruto's summoning), but that still doesn't explain why they don't show the seals for chidori or kage bunshin (kage bunshin DOES require multiple hand seals. It's in one of the episodes when Sasuke and Naruto fight against Haku).
Anyone got an answer to this? I'm fresh out of ideas.