Logging multiple gigabytes of data with Arduino
I'm not sure where you have the impression it won't work. I haven't used 64GB cards, but have used 32GB cards and they work fine in terms of FAT32 and writing files.

As you have already worked out, reading or searching the file system can get very slow as size increases.

That said, I have found that larger capacity cards are more likely to have problems with the SPI interface being poor quality. Consumer devices do not use the SPI interface, and it seems that some manufacturers are willing to skimp on this side of it. The SPI interface can be buggy or unstable as a result. Genuine name-brand cards should work fine though.