I am having the same issue. I recently reinstalled after getting back to the playing the game after a year or so with the Lay D Denton mod installed, because the game was way too fast. After reinstalling the game now keeps heavily stuttering, with or without mods, no matter what settings I pick.
EDIT:
I figured out how to fix the problem on my end. The LDDP Mod I mentioned above happened to include advice on how to fix the stuttering issue. I'll quote the relevant part below, hope it helps:
1. Open up the game.
2. Open the console. By default, you hit ‘T’ or ‘Y’. Backspace to remove everything and then type
“preferences”. Hit Enter.
3. Go down to the “Rendering” Submenu, then to the “Direct3D 10 Support”
4. Enable these settings:
a. Set "FPSLimit" setting to zero.
b. Set "Precaching" to "True"
5. If that doesn’t help, open the NVIDIA Control Panel. Go to “Manage 3D settings”, then the
“Program Settings” tab.
6. Under “Select a program to Customize”, add deusex.exe to the list.
7. Change the following settings under “Specify the settings for this program” (you may need to
change the preferred graphics processor first):
a. Low Latency Mode: Ultra.
b. Max Frame Rate: 120 FPS. (I chose 60)
c. Power management mode: Prefer maximum performance.
8. Click Apply.
Post edited 4 days ago by Gigalomaniac