When does a Scrivener project get too big?

‘Anne’, I realize my comment here is nearly two years later and mostly dealing with Windows v3. (Your version being 1.x?)
I also understand that my comments are more operational than organizational.
(I have a Notes folder, one for Considerations, topic folders, and several Collections; Three MSs.)

My principle project (‘Works’) is rather larger, not so much in data size (366 MB), but in its number of files/folders (27,655 / 25,274)!
(The files in Works range from one-liners to Montesquieu’s 270k words in The Spirit of the Laws.)

An ‘All’ project search in Works (not Trash) with three terms (Aristotle Aquinas rejected), takes about 10 seconds; a ‘Text’ search takes about five seconds.
(In v1, the ‘All’ search takes about five seconds.)

I am told by LL support that the conversion of Works from v1 to v3 took quite a while. (I’d sent support a ‘copy’ of the project due the issue below.)

I have another v3 project, Stacks (Journals), much larger (605 MB)
but with far fewer files/folders (737/779), research journal articles. The same search (Aristotle Aquinas rejected) takes about two seconds.
(This difference is likely understandable.)

‘Works’ has about 30x the files as ‘Stacks’ and its search indexes are about 57.5 ‘MB’ compared to Stacks’ 18.4; about 3x the size.
Works is also different from Stacks in that the latter’s files have no links to other documents; many of Works’ documents have many, very many.

While none of this above is an actual frustration – there is much about v3 besides that I greatly appreciate – there does seem something about Works (it alone of my four working projects) that changed significantly from v1 to v3: I have to avoid any menu-item (mostly) that builds a file list, lest Scrivener hang for about 24 seconds to build the list each time. (In Works; my v3 Stacks brings up such submenus immediately.)
Fortunately, I am generally a keyboard navigator, lest I inadvertently drag the mouse across such a submenu item too slowly.

Broadly, it appears that fewer, (much?) larger files is better, combined with or otherwise that (far) fewer links are?

Why do I have sooo many files in Works? Because, in my writing (non-fiction), I relish the serendipity of both factual and fictional results whenever I search.
(I’ll admit it is also a bit of a research shortcut.)

(Yes, the backup takes time: I do mine at closing.)


ps: Some of my communication with LL support on this generally:
[Finding elements after Scriv3 project conversion - #4 by dbc183c7]

Win 10 Pro x64 [19043]; i7 7700, 32GB RAM, 2T internal drive.