How should a non-native English presenter respond to a question they did not understand?
Yes, it is appropriate to ask the questioner to repeat the question, prefaced by:
"I'm sorry but I didn't understand the question. Can you repeat it or rephrase it?"
If you still don't understand it, you might ask someone else in the audience to restate it or rephrase it.
Some people at academic conferences are not good at asking clear, direct questions, even when they are native English speakers with normal dialect. I have asked people to repeat or rephrase questions for this reason, and I am a native English speaker.
As with the other answers, I will echo that it's OK to not understand and to ask for somebody to repeat themselves. Even as a native speaker I often have a hard time understanding a question.
Sometimes, though, it's not because the question's hard to hear, but because the reasoning behind it is odd or because the question is just not coherent to begin with. As such, I want to add one other strategy: if I still don't understand the question after one repetition, I will simply make my best guess at a reasonable question I think they might be asking, saying something like this:
If I understand you correctly, your question is about why llamas prefer melons over grapefruit. The answer to this question is that ...
This way, I'm giving a good answer to some interesting question, and it might even be theirs. If they're satisfied, great; if not, they can try to clarify their question. Moreover, because I repeat the presumed question back, it's hopefully clear to the rest of the audience that if something's wrong it's with my ears (which are not scientifically important) and not my thinking (which is the important bit).
I have never come across somebody who seemed to be using difficult expressions just to confuse a non-native speaker. When people talk to you in complicated English, it's because they haven't realised you might not understand, and that is quite likely because your own English is good enough that they forget you don't speak the language perfectly. Just say something like, "I'm sorry but I didn't understand all of your question. Could you repeat it, please?"