That was really just during the N64 and GameCube eras, when Land 2 came out in 1998 it introduced the short sleeves for Wario, something that stayed consistend in the Wario series, for whatever reason it just took forever for other games to make that the default and is some cases it was rather inconsistent, he had short sleeves in Mario Tennis 64, but went back to long ones for Power Tennis for instance.
However eventually they caught on, particulary noticable with Mario Kart Wii, which reused Double Dash models, but went out of it's way to make Wario's sleeves short, instead of keeping them long like in DD.
No idea what made them decide to finally stick to short sleeves, but it has been consistent since then and must must have been a conscious decision.