All that will do is check that the nand.bin's sha matches the bin.sha file; this doesn't really ensure that the bin isn't bad [i.e. a corrupted dump] as the sha's would still match; and besides hourglass9 checks the shas before flashing anyway.
What you'd need to do is dump nand twice and check they're identical - via the sha's.
Checking the sha's on PC I guess would be useful if you are using a version on decrypt9/hourglass9 that doesn't have sha checks.
Hourglass9/Decrypt9 probably generate the hash while reading the NAND, so if any corruption occurred on the SD card even if it was during writing, the hashes wouldn't match. The chances of reads failing without an error, leading to corruption, are infinitesimally small, it's much more likely to corrupt during writing.
You are right though, if someone is paranoid and wants to be 100% sure then making multiple NAND backups is the only way.
But something would have to be wrong with the NAND itself for the reads to fail (unless there is a serious bug in the homebrew apps) and at that point you are pretty much screwed anyway.
Anyway, in OP's scenario (bad SD card), the SHA checksums wouldn't match and a checksum tool would tell him that, so I think it answers his question.
Verifying the checksum on a PC wouldn't be necessary in most cases, except if someone forgot to copy over the .sha file they wouldn't be able to tell if a backup was corrupted.
