While reading up on V.A.T.S on Fallout Wiki, I've stumbled upon this:

VATS targeting is bugged for certain guns - most lever action rifles and a few pistols: it consistently shoots high, making headshots improbable or impossible. Consistently replicable by starting a new game, adding a brush gun (id: 00121148) and .45-70 ammo (id: 0013e43e), forceaving guns to 100, and shooting at Easy Pete's head from the nearby road. Bullet impacts will appear on the windowpane behind him - and, shot after shot, will consistently be high. Modifying the gun to have perfect accuracy and/or setting fVATSSpreadMult to 0.01 will reveal that the VATS point of aim is roughly a foot high. No known fix yet. This bug also seems to occur with the Hunting Revolver.

Has anyone actually noticed this from their gameplay experience? If yes, any idea where to get a precise list of affected weapons?

Yes, all leaver-action weapons and revolvers. Can even shoot high in free-aim at times.

just wondering... do they ever aim to fix this since it makes cowboy perk useless and well this is bad

I don't know about that. I use VATS a LOT and have had no problem with the Lever Guns. Cowboy Reapter, Trail Carbine or Brush Gun. If you are using VATS they are the best. And I have never ran into that bug.

It's really bad on the PC version. 50/50 shot of it happening, or another VATS bug as there are many, when firring from a crouched position.

EDIT: Don't use VATS much and it's not really an issue. The free-aim animation malfunction that cause it can be avoided.

No, I don't expect Obsidian to ever fix this. It doesn't cause a CTD/Freeze so not worth the resources to correct.

VATS doesn't work worth a damn in NV, I only bother with it at point blank range and even then only if I'm facing multiple opponents. There is something wrong with it, VATS in FO3 worked a lot better.