Take a look at this answer. Personally, I do upvote similar comments/answers that have some sense of humor from time-to-time, but is it fine?
Updated sample comment
You're free to vote however you want. If you want the site to be as clutter-free as possible, then don't upvote them. If you want to reward the comment/answer an upvote since it made you smile or laugh, upvote it. The decision is yours, and the mods have no power to control how you vote or why you vote the way you do.
As for me personally, I wouldn't upvote an answer that did not answer the question, no matter how funny it was.
The example is something of an old relic, but I don't think it would fly nowadays ;-)
Upvotes, however, are totally a personal and subjective matter. I mean the choice, however the officially sanctioned "rules" of upvotes are exactly what the screentip tells you -
This answer is useful
So if was useful to you, by all means up-vote.
That said, be more liberal in upvoting comments than you are in answers/questions. Why? When you upvote answers/questions you're slowly conferring real power to that user. So don't push a user who is simply a comedian into wielding deletion powers
And just to solidify to you how the community feels about "sloppy" voting, I asked about whether it was ok that I upvoted new posts based on apparent effort. I got -13 , so... yea.
May people have written requests to allow commenting for low-rep users. They've generally gotten answers like that: https://meta.stackexchange.com/a/71390/155074
We funnel users to the answer input box for a reason -- because the focus is on getting answers to questions, not meta-commentary. Commenting is a privilege that should be earned by providing useful answers. And 50 rep isn't much
The comments are considered the less important member on StackExchange sites, so, consequently, votes on comments aren't as important either. I think we can safely assume, that the rules for voting on comments are also more loose (most of us assume that already).
The answer should be useful in order to be upvoted, because the answers are crucial to SE sites. Comments are only addition, so feel free to upvote those, that are just a nice flower to the sheepskin coat (a Polish saying).
I think your example is just because meta is a slightly laxer culture than SO. Perhaps this is a bad thing because it sets a bad example; perhaps it's not that big of a deal. In any case, if you see something silly on meta, you shouldn't take it completely seriously as exemplar behavior for the SE sites. That's the fact of the matter.