This has been a fairly clueless discussion:
1. Waterfox is the 64bit version of Firefox built and maintained by a separate community independent of Mozilla. The main advantage of 64bit programs (any programs) is that they are able to use more memory (more then 3 or 4GB depending on who you ask/how you think about it) than the implicit register limit imposed by 32 bit programs, like Firefox.
2. I see absolutely no reason why OP shouldn't be able to open 3000 tabs if he/she so desired, so I'm not sure that just because his usage case is foreign to you, means that it's not a valid question - it is; I myself tend to do a combination of 4 different browsers open at the same time, bookmarking tabs I close, or suspending them using a few suspension addons, but I'd say I have a few hundred open across the browsers at any given instant in time. The reasons I do that aren't really relevant either.
3. The concerns of Waterfox having "viruses" etc. are very unfounded; it has a fairly active userbase, and indeed, there are those that claim that IE is susceptible enough to to malware to qualify as 'having a virus' just by using it. I suspect anyone saying this just doesn't know anything about Waterfox, or similar browsers (e.g. PaleMoon).
4. As to answering the OP's actual question - YES Waterfox will be able to use more of your RAM, and won't be limited to the 2GB or so that I believe Firefox instances tend to clock out at. However, whether this will allow the stable running of so many tabs - more than say, a few hundred, I'm very suspect about. The reason is actually very simple: The program (most programs for that matter) doesn't simply scale linearly with more memory - it's not as if each 'tab' uses a certain amount of RAM and that by simply increasing RAM usage you can therefore maintain the same program stability/performance that you would see if you were using it more in line with its design specs (which, I suspect, are probably something like <250tabs open, ceteris paribus).
Many elements of the program's software architecture come into play in this problem - simply increasing the RAM availability then, simply won't be able to compensate for performance degradation that is actually a fundamental architecture problem. Java threads, flash instances, the program's own plugin container, the OS/program memory management (infamously problematic in ALL browsers, Chrome/Safari/Opera/IE/Firefox, etc.), and a few other things I'm not well versed in, all WILL affect how the program performs, regardless of RAM availability.
5. Finally - I happen to know that the current release of Waterfox has a weird quirk/bug which has nothing to do with RAM, and while the program works fine (as it always has), it tends to spike on CPU usage (this has been noted I believe on the dev page) for some reason that I can't figure out. It actually led to it being a problem, and so I'm waiting for them to correct this. Also note that you cannot use Firefox AND Waterfox at the same time; they block each other.
6. As a solution, assuming you don't use PaleMoon which I've never used, you might consider, (I have no idea if this works) opening MULTIPLE INSTANCES of Firefox (not just opening new windows - see the Mozilla page for how to open a new instance with a new user profile); this MAY (MAY!) bypass the RAM limit on each Firefox instance, allowing you to feed each instance a full bloc of RAM, and possibly avoiding all the aforementioned issues. But I don't know if Windows will allow that to happen, or if indeed Firefox can actually be 'tricked' into segregating itself into completely separate 'programs' which call their own RAM reserves from the system pool. I would say - try it!