Definitely better late than never! ESPECIALLY if it's something important like an RP-related matter, or anything else that I clearly wanted a reply about. If it's just some casual conversation that someone stops replying to, then I probably wouldn't care either way -- but if it's something like "Hey, are you still interested in this RP? You haven't posted in a while" then I DEFINITELY want a response. Late is most certainly better than never. I don't even care if the answer is "yeah no sorry, I want to drop out" -- I would actually greatly, greatly prefer such a reply to mere silence.
As a GM, I can't tell you how much it drives me insane to see people avoid mentioning these things because they think I'll be mad or something. @_@ I try to emphasize as much as I can that I would so very very much prefer people being honest about wanting to drop-out than to be left in silence, and yet, it still happens. DX I can understand why some people might feel guilty about admitting such a thing, or fear that I might get angry, but, I won't. I just want to know whether or not people are still on-board. It's perfectly alright if the answer is no. The most I could do to change someone's mind is perhaps offer an "are you sure?", and then try to get them feeling inspired again if they say that they're not totally sure about leaving, or otherwise give me reason to think that there's some small thing I could do that would make them want to stay. But if people really want to leave? I won't stop them. The only reason I might send multiple reminder messages is because I want a reply.
So yes, late is definitely better than never. Especially if it's only two days. I mean, that's practically nothing. Plus, I'm not sitting around with my eyes glued to your profile wondering whether or not you've seen my message yet. At least not after only two days, anyway. If it's been weeks and you haven't replied, even though I can tell that you've been online and active all that time, then, yeah, that'll bother me a little, but I'd rather get a reply that's two weeks late than four weeks late, and I'd rather get a reply that's four weeks late than never get a reply at all.
And you have to be a special kind of evasive to make me want to yell at someone for a late reply. Nine times out of ten, I'll be happy that I got a reply at all. I might ask why it took them so long to reply -- if the reasoning wasn't already made clear -- but that's usually only because, when people take an absurd amount of time to reply despite being active the whole time, I can generally only assume that they either forgot about my message, or they're too afraid to respond -- and the former becomes more and more unlikely with each consecutive reminder sent. If I ask, it's only because I want to know what the problem is, so that I can fix it -- especially since I really, really, really don't want people to be afraid to message me about these things, and I will tell people a thousand times that I would greatly prefer an answer over silence if that's what it takes to get the message across.
Sorry if all the GMing talk is off-topic and/or not what you were going for, but it was definitely the first thing that came to mind, and I certainly wanted to throw all that out there in case the fear you mentioned about replying late does extend to GM's, as I'm probably not the only GM who feels this way. O_O
In more casual contexts, I wouldn't really care much either way. If it's just some conversation that you forgot about, then I probably won't even notice or care if I never get a reply. If you do reply late to a conversation like that, then, well, I certainly have no reason to be angry about a late reply, at the very least. It just... doesn't make a difference to me. Do whatever you want to do.
But if we're talking about RPing, or if there's any other important thing that I clearly want an answer about, then yes, message me. Late is a thousand times better than never. Honestly, there have been times when people have messaged me months after the fact -- long after I'd already assumed I was never getting a response and did away with their characters or whatever I needed to do -- and even then, I wasn't mad that I got a reply. If anything, I actually really appreciate seeing people take the time to clear things up with me even all that time later. There's usually not much I can do about their spot in the RP after all that time, but, it's still nice to see that they cared enough to say something.