Seems once you hit 100 bananas, instead of reducing to 0, it instead reduced to 66. I think it might have something to do with BCD calculations (Binary Counted Decimal that represent hex values as if decimal, 8-bit ranging from 00h to 99h, whereas 8-bit binary number ranges from 0 to 255 expressed as 00h to FFh). While I haven't figured out the problem with DKC2, I believe I may have fixed Secret of Mana regarding shop buying/selling.
edit:
DKC2's banana problem fixed, at least it seems to be. It at least reset to 0 when you hit 100 bananas.
Regarding the fix for SoM shop pricing, you may notice that if you sell all your stuff, the last item you sell won't update your funds on-screen, and you won't get the usual jingle that happens when you do sell. Don't worry. Internally, the game has the correct amount. It's just not updating. If you exit the shop menu and re-enter, it'll reflect the correct amount, or if you buy something immediately after while still in the shop menu, your remaining funds will correctly be displayed after the purchase.
At first I thought this was a problem with blargSNES emulator, at least I think it is, but I just tested the exact same thing on Snes9x, and sure enough, it happens there too. So unless it happens differently on real hardware, I'm just gonna assume it was an oversight by the developers.