Super def. up not so..... super?

Not exactly true. It deals 1 damage, but it doesn't lose its auto-kill property.

So on a boss I'm pretty sure it'll still do just 1.

It does its normal full damage on bosses, even during Super Def Up. This has already been pointed out by Marksman. One MM was even so kind as to prove it by saying it's really easy to test on Geist Balrog. If you use Snipe on it during its Super Def Up, you'll see a 1, but the HP bar will still drop a noticeable chunk.