Thanks for your reply!
Reading the app note, I found what I had to do to get my signals working: I had to DISABLE incremental compilation at all for my Nios II taps! Then I got a warning message similiar to the following:
Some SignalTap nodes are of type post-fit, but this type can only be used with incremental compilation enabled. All post-fit signals will be treated as pre-synthesis signals.
This of course, rendered all my post-fit taps (luckily not too many) unusable ("signal does not exist in design"). I had to change these signal names (they usually ended with something like "signal_name~17") to their pre-synthesis eqivalents (just "signal_name") and it worked quite fine after that.
I have to say that all this is rather annoying. Especially after disabling incremental compilation, the compile time has increased by 30 to 50%.
And now another problem has appeared: Quartus crashes when opening, saving or changing my SignalTap file in some ways... haven't found a solution so far, but it has to do something with the Nios II plugin's mnemonic table. I issued a mySupport service request.