Puresabe's Rockman 6 Optimization patch does that. Apparently the problem is that the game tries to play the regular shot sound and the charge shot sound on the same frame, and the charge shot sound gets overridden.
It's uploaded on his site: http://borokobo.web.fc2.com/
And if you want to customize the patch, you need an assembler like this: http://www.2a03.jp/~minachun/nesasm/nesasm_x86.html
I compared two patched ROMs, one with the sound effect fix active. All it does is this:
6D715: 07->08 Raise priority of reflect sound so charge shot sound doesn't play over it (US offset is 6D7F1)
6D725: 07->08 Raise priority of charge shot sound (US offset is 6D801)
70CD3: 28->23 Use uncharged shot sound for partial charge shot instead of charge shot sound (for personal taste)