Because if you don't show up they could send you to jail anyway without you having had a chance to make full defense?

I was taught that trials in absentia are not really a great thing.

The problem is evidence and particularly eyewitness testimony (unreliable to begin with) decay with age. Banning absentia trials creates an incentive for people to hang out for a few years, then come back and say "all this evidence is too old, you should reasonably doubt its integrity".

Was the Pirate Bay trial(s) subject to any of those weaknesses?

Dunno. I thought the thread had wandered away from a specific case and was making a general comment. But yes, I believe that's something considered before proceeding in absentia.