It looks like most of the drives will have a jumper for a 512-byte compatibility mode. This mode may not offer the full performance benefits, but then again, the drive is so much faster than the Amiga interface, I'd be highly surprised if there would be any performance hit by enabling it. So just put the jumper on, the drive presents its logical geometry as 512-byte, problem solved. (Well, other than how you'd recognize 2TB of storage...)
Yeah, I don't think that there will be a problem with larger block sizes, but 2 TB is probably a dead end for most IDE/SCSI device driver. Poseidon's massstorage.class supports even larger drives than 2 TB (in theory, I could never test it), and also supports an emulation mode to convert the 4 KB blocks back to 512 blocks if the app needs this (some filesystems do, such as FAT95).