I've PC gamed since ~2000 (I had to force myself to turn my Dreamcast on and finish the Shenmues but it was worth it) and don't recall ever having scanlines visible. I think they only showed if you had to use much lower resolution than your CRT monitor's native by then. I didn't dabble in emulation back then to see if playing say SNES and Neo Geo games ran at low resolution got nice scanlines naturally without filters, that's a shame. Of course you'll want scanlines even for modern native PC games if they're low res pixel artsy (and they usually offer options), I'm just speaking for the average 3D game Dreamcast onwards here.
I never thought to add scanlines when playing older 3D PC games except when using dgVoodoo2 for Star Wars: Rogue Squadron 3D or similarly ancient titles that don't natively work in Windows 10 and I didn't stick with it. I guess I'm weird given that sort of game is definitely pre-Dreamcast era. Maybe I'd use scanlines for the N64 version but perhaps the longer draw distances and detail levels afforded by PC of that time means it's better in high resolution. I guess a 3D game that can't be ran in native high resolution and defaults to some 640x480 could be better with scanlines but in the past when running lower than native games like Diablo II or Baldur's Gate (not EE) I enabled windowed mode (if unavailable set the GPU to center the image) instead so that they're not stretched to full size.
Of course if you have like a 4K monitor they'd be tiny windows so you might want a different approach.
I don't often play PC games much older than those two. Beneath a Steel Sky is one I played but forget if I used SCUMMVM filters. I think it's possible I used scanlines to double the image size while still playing windowed or something along those lines. Actually that was my approach when emulating the likes of GBA years back before RetroArch, just use scanlines2x or similar. But I guess newer games like Trails in the Sky would qualify given they're very PS1-like in low res visuals (but support high res for their 3D) engine, yet I didn't feel the need for scanlines there either. I guess I'm weird. It's up to you what looks fitting