(Massive post follows, but there’s a TL;DR at the end.)
namely:
I think this is (like many other things!) a matter of taste, though; I like nested hint systems, and coy/cryptic/rhetorical questions are useful to me; it’s often happened that the first coy clue has made me slap my forehead and go “of course,” which is a lot more fun than just having the solution revealed. Having to go to an external webpage and highlight text to find an answer sounds more annoying than going through a hint menu to me.
Wade’s point about the design of the menus is a good one, though. There was one game last year where I had to use the hints a lot, but the hints were at the bottom of a menu that included the introductory material, and then the hint menu itself had a lot of “general hints about IF stuff” (try examining things!), and then there was a topic menu, so that the actual hints required paging through four menus. I never finished that game. The usual menu extensions don’t seem to support “press a key to go straight to this choice,” though; it’d be great if someone added that functionality. Though I understand that she’s very busy.
The transcript issue is something that I don’t really care about, but again YMMV. I certainly wouldn’t want a game to give me a hint system I liked less in order to make the transcript look nicer, but then again I usually forget to take a transcript at all. One possible solution was the one “Cursed” did last year, where the hints were actually a separate game file; assuming your interpreter lets you keep two game files open, that seems that it could avoid cluttering your transcript, and also let you keep your place in the hint system. Or you could have an in-game hint system as well as one that runs offline; as maga said, try to reach as many people as possible.
One thing about nested hint menus though: You must, must, must give the solution at the end of the menu. There’s nothing more frustrating than being stuck on a puzzle because you know what to do but not how to communicate it to the game, paging through umpty-ump hints, and finding that the last one tells you what to do but not how to communicate it to the game. (Unfortunately, “Cursed” did this; there was a hint sequence that told you that you needed to do something to a certain object, but didn’t tell you the very guessy verb that you needed to use.)
Contextual hints can be great but they also require a lot of work to make sure they go smoothly. On a couple of occasions I’ve been playing a game with a contextual hint system that for one reason or another just stopped offering hints in the middle of the game. (Once I’d triggered a bug that I could get out of but that broke the hint system, once I think the game considered that I’d solved the puzzle but I didn’t know I had to go to a certain room to reap my reward.) If you’ve got one of these, test it a lot.
TL;DR: The hint system is part of your game and will be part of many people’s interactions with your game. Give it a lot of thought and design it well. You may decide that for some reason you want to give minimal hinting, that it’s better for players if they have to wander around for a while before they figure out what’s going on – but if you do that, you’ll frustrate a lot of people. And you probably have to have established a lot of trust for the players to feel that it’ll be rewarding to bang their heads against the desk until an idea shakes out.