Ok, time for Sunday rant (tm) (c)
This is an SDHC card we're talking about. Designed to be used as portable, interchangeable storage. It is NOT an SSD, there is a reason why those cost a lot more for comparable capacity.
So the very good reason these cards use FAT32: it can be read AND written out of the box on any Mac, Windows or Linux box, in any camera, GPS receiver, MP3 player, eBook reader etc. That's the whole point. The built-in controllers were designed with that in mind, and also because FAT32 is a simpler, more efficient filesystem to deal with.
Ext3, NTFS, HFS+ are all nice filesystems, but there is little point for that kind of I/O overhead (journaling etc.) on a simple device to easily take files from one box to another, again: not an SSD to function as a full-fledged system drive. (Ext2/3 would be the most likely candidate, since the other 2 are proprietary and not working that well on Linux, even if they exist in working form)
From a practical perspective, 32GB cards aren't even up to class6 speeds yet, which isn't exactly fast to start with. Lower capacity cards meet or exceed that speed easily. So perversely the more space you have to write to, the slower it gets. I could afford 32GB cards but can't be bothered to buy them because of that.
16GB is plenty capacity for an -eBook reader-, and the 4GB filesize limit is plenty too. If you have a single PDF file that's more than that, you should rethink your document-deployment strategy (and I doubt it would be usable on the DR1000 if you could fit it on the card) We're not talking about DVD images and HD movies here. I already have thousands and thousands of files on there (a lot of images, since the DR1000 can't read from compressed folders; now THAT would be a -useful- feature to add file-wise)
There will be no 64GB card in SDHC because 32GB is the limit of the spec, just like 2GB was for SD. There will be perhaps a new format in the future, and it will most likely be as incompatible with SDHC as that was with SD (and I have a pile of useless cardreaders lying around to remind me of that)
(They recently announced a 64 Gb (Giga-bit- =8GB) memory chip which means half the chips for the same capacity)
In short 16GB (or 32GB if you have to) in FAT32 are fine. Back up your data if you are worried about reliability. Just because you can do some things doesn't mean it's a good idea. And perhaps the DR2000 will have a whole new level of memory-card technology built in.