30 minutes compared to what? Personally, I get that resynthesizing the SignalTap and refitting takes some time. (You can disable timing analysis to save a little more, if you're confident). I would really like to see a way to just re-route the signals from the user logic to SignalTap incrementally, which I believe could be significantly faster.
There's a lot to be said for pre-synthesis, but there is the obvious expense of having to resynthesize and fit everything. I've seen user's put keep attributes on the pre-synthesis signals they commonly like to tap, ensuring they're around as SignalTap post-fit nodes.