The checksum being reported from SNES9x is the internal ROM checksum. This is an entirely DIFFERENT entity from the target ROM file hash (MD5/CRC32) reported on the hack's page. Secondly, the hashes being reported on the hacks page are for the ORIGINAL ROM that the patch is for (without the header). It is NOT the hash for the resulting patched ROM.
In summary, to match the ROM info, check the original ROM without a header and they should match.
The internal checksum reported from SNES9x is internal ROM data that hack authors may or may not choose to update. So, it is possible for it to be reported as bad, but you still have a correctly patched ROM. Because the internal checksum is an unreliable indication is why the community uses target file hashes instead.
In your case, the patch author did updated the internal checksum data from the original ROM for an extra layer of confidence (many do not bother) and it does report as good. So, your ROM is likely patched correctly!
This may seem a little confusing at first, but walk through it and you'll get it.