My guess is that the MSX was popular in Japan, and the Amiga was not.
Astute observation, but it hardly answers the question. As far as I understand, the participants in the MSX game contests are mostly European and South American.
My own idea is that the Amiga community in its bulk consists mostly of hardware collecting end users, and on the creative side we mostly have OS developers and some demo coders + Amiga musicians still active. This in its turn is possibly a result of the relative complexity of the system (compared to the more active 8-bit machines) and the hardware modularity/expandability.
The Amiga community might be divided in too many ways for game competitions like these to ever be possible, not to mention hardware. Amiga 1200, Amiga 500, AGA, ECS, graphics card, no graphics card, RAM expansions, register fiddling vs APIs, OS3, OS4 MorphOS, Power PC, 68k. In an already small community, differences like this can be devastating for collaborative effort.