Meaning of "quick reply"

"Quick reply" is not a special phrase. It is simply a "quick" reply. "Quick" here means:

Quick: immediate or prompt

So, it simply means a reply which was quick (prompt/immediate). Whether you appreciate someone's quick reply or not, would depend on the context of the argument. In "thanks for the quick reply", you usually thank someone for responding quickly. But it could also be used sarcastically (as I said, all depends on the context).

I look at "thanks for the quick reply" without context and it does seem as though it could have sarcastic intent to me. However, I think this could be corrected by simply changing the informality of the "thanks" for a more formal "thank you"... although if you are still uncomfortable you might use the words "speedy" or "prompt".

I'm sorry, but I think that this is largely a matter of context which could hold an almost infinite amount of sway over the final meaning of the phrase.

It always means the first ("timely"); it may also mean the second ("not necessarily well thought out").

If you give a reply quickly, that may mean that you have not devoted adequate time to formulate a complete answer. But the key word here is "may". It depends on context and phrasing, and sometimes a bit of insight on the part of the reader. On the obvious side, if you ask someone for his phone number and he replies in twenty minutes, that is likely "quick" purely in the sense of "timely". But if you ask someone to write a complete history of the world from creation to today, and he sends a reply in twenty minutes, he either copied it from someone else or just threw together the first thing that came to his head.