TrueCrypt: filesystem corruption: is it possible to lose all data at once

That corruption may happen if you disconnect your drive before all of the data was written. TrueCrypt acts as a middleman, encrypting/decrypting data on the fly as it is read/written. It does not affect the way your OS or programs write to the disk.

So, if some program write()s a lot of data without flush()ing, and you disconnect that external hard drive, some data may be not fully written at that moment. But it has nothing to do with TrueCrypt.

If windows, or the program you are using doesn't treat removable media in some special way, then there is no difference how you mount that drive (beyond those pesky folders).

Encrypted backups do have their drawbacks. In case the backup media becomes corrupted, you may lose everything whereas chances are much better to retrieve unencrypted backups (at least partially) from a damaged disk.

In any case, only one set of backups is insufficient. And if applicable, maintain an unencrypted backup in a safe location (e.g. a bank vault). Security comes at a price.