Yes, they do mean the same. I think What kept you? sounds a little more critical than What held you up? NB you don't need to include 'has' in these phrases when speaking. Hope that helps!

I've never heard someone say "What kept you". It may not be incorrect, but I don't think that it sounds right. It would be more common to use 'kept' when you are referring to sleep. For example "What kept you up all night?" or "What kept you from sleeping in this morning?" That's my understanding of the usage, anyway. If someone is late, I think your first example is more appropriate, though I may rephrase it to read "Did you get held up?". It just sounds more polite.