Well, I did some further testing on this with later D3D6 applications. The applications are some fairly obscure but not demanding games (for a V5), of which the most notable is perhaps Turok 2.
The symptoms are comparable to what I described for G-Police on V3: The games run with decent framerates, but while moving or turning it just slightly stutters. This behavior is far more noticeable on higher resolutions; in plain language, that means that getting some ancient D3D games in 640x480 to work without hitches is no big problem, but contemporary D3D6 programs in 800x600/1024x768 (some also even in 640x480) just suck. It doesn't "feel right", if that's a comprehensible category.
This is all in relation to Glide gameplay, where I get far more coherent (and of course overall much higher) framerates even in games such as Unreal. With "too" demanding settings/resolutions (lots of FSAA etc.), it just plays with a lower framerate, but in a somewhat more uniform fashion; still far more enjoyable than the D3D stuttering. To sum it up, Glide really "just works". OpenGL was generally no problem too, I played through Quake II and Hexen II on V3@1024x768 with the ICD and had nothing to complain about. Didn't test any more OpenGL stuff besides that though.
On a further note, Turok 2 in D3D6 had noticeable glitches, which were absent in Glide, but that's more of an individual game thing I reckon. Generally speaking, the Direct3D image in any title that also supports Glide looks bright and washed out in comparison to that.
From my testing I can only conclude that there are four possibilities:
1.) D3D performance on 3dfx cards sucks in relation to its competitors from the time which were rather more dependent on the API, and I would not get any of these problems with, say, a TNT2 Ultra.
2.) Early D3D just generally sucks with contemporary cards and I would see all of this on just any card from that time.
3.) It's related to my monitor or something arbitrary like that. I don't see how this could be when all Glide titles are running fine. Maybe due to being able to set the appropriate refresh rate with Glide contarily to D3D...
4.) The cause for this is my DX9.0c installation, and, say, default Win98SE DX6.1 or DX7 would work fine. Well, I may give it a try with DXBuster when I ever feel like it. Fortunately I'm not really after Direct3D titles which are better played with Glide anyway, it's just more of a curiosity type of thing...