yes, the 64-bit version of MPC-HC is known to be slower. It's recommended to use the 32-bit version since it's faster and more compatible with everything like quicktime and such...
MPC itself has little to none assembly. But ffdshow and MPC's internal ffmpeg decoders do. And yes, those contain a smaller amount of optimized assembly code in 64-bit builds.
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Furthermore it doesn't necessarily work across operating systems either. From what I read here 64bit assembly written for linux won't work on windows without changes and vice versa.