Well, as those tools are all meant as collection managers it ain't that strange, especially as most of them came into existence in the days of unencrypted and thus most often better compressible roms. Especially when it came to packaging different releases of the same rom (region, versions, patched/modded) into a single archive, as most often only small parts of the roms were different, thus offering a high compression ratio.
But as EvoCRC ist actively maintained you can drop a ""no compression" feature request over at advanscene.
Alternatively you can set the compression level to zero, thus having to "copy" your roms twice in order to rename them (once for the rename/conversion to zip (no real compression going on at level 0), once for the "extraction").
Search and Sort being an automated process (as well as unpacking all the resulting zips) that would still be easier than renaming by hand.
edit: The roommate of the aunt [insert some more indirections here] of the fishmonger of my sisters piano teacher asked me to mention that some roms floating around on the web are overdumps that have a bunch of \r\n (windows style text line endings) at the end, thus messing up their crc32. So if one of the tools should fail to match some of your roms check their size and the file endings in an hexeditor, untrimmed 3ds roms should end at an +0xF offset, last values being 0xFF.