Just taking the word of the sites mentioned by Enig and of the Wiki article, I voted yes. But I sorta believe that very early on, Haunting Ground became something else that was still very intentionally related to Clock Tower.
Having just beaten the game (literally, less than three hours ago) it seems to me like Capcom realized they couldn't very well make it a sequel, because it's almost like they were fixing what they saw as mistakes they'd made with Clock Tower 3. There are too many similarities between the two games' plots to be mere coincidence, I think.
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Both Fiona and Alyssa were targeted because only by killing them could some mastermind obtain immortality, a master mind who was the grandfather of the protagonist in both cases, and who the protagonist trusts at some point, in one form or another, to be helpful.
In both video games, the very reason the lesser enemies even exist (or in CT3's case, continue to remain incarnate) is because of the said Mastermind, who is using them in some way to further his goals, not only in a practical way--i.e. to kill the protagonist--but as in he derives some benefit directly from the lesser enemies quite independent of the protagonist; research/experimenting in the case of Haunting Ground, power in the case of Clock Tower 3.
In both videogames, that Mastermind (for the most part in HG, and totally in CT3) maintains his articulate composure even as he becomes the final enemy, unlike the earlier, less articulate enemies.
In both videogames, there are unnatural objects that are dangerous to touch, or else the protagonist will attract the stalkers and go up in panic mode; the butterflies in CT3, and the blue orbs of light in HG.
Both plots feature the protagonists parents/parent being killed specifically because one parent had passed on something special to the daughter, and would presumably pose as a more savvy, knowledgable obstacle for the antagonist if left alive.
Now, many of those similarities I would chalk up to merely gameplay similarities or genre similarities, if not for the fact that Capcom made both games and surely would have been deeply aware of these similarities. It's almost like someone at Capcom thought, "What if we took the basic outline of CT3's plot and tweaked it so as to better capture the spirit of the original Clock Tower games, like fans have been asking for? Because, it seems to me at least, that Haunting Ground is, in many ways, what a less fantastical, more confined and lonely version of Clock Tower 3
would look like. If you strip Clock Tower 3 of multiple (particularly time travelling) locations and the human interaction Alyssa has in Dennis, it'd already begin to feel more like Haunting Ground.
Hewie is the biggest addition, but then, since once production began, Haunting Ground wasn't supposed to be a Clock Tower game anymore, that big difference could be explained easily, as well as by the fact that Hewie gives Fiona a friend but while still making you feel isolated, since you have no human companions...
So I guess I think Haunting Ground is not only possibly a tribute to Clock Tower despite not being released as a Clock Tower, but a "what-might-have-been" regarding Clock Tower 3. And though I'm glad CT3 exists, if Haunting Ground is a "what-might-have-been" then it certainly captures the spirit of the Clock Tower duology better, particularly the isolated "I may be the only sane living person within these walls" feel of The First Fear. Haunting Ground is awesome enough for me whether it does or doesn't have anything at all to do with Clock Tower; but it's still a very interesting thought if it does (in spirit).