In order to prevent slow down (despite the game reporting 60fps) on Steam Deck:

1. Install the latest version of the Restoration Project Updated (RPU) or the Unofficial Patch Updated (UPU)
2. In the game's install directory, open f2_res.ini and make sure both UAC_AWARE and GRAPHICS_MODE are set to 0. This file is also where you set your preferred resolution.
3. In the same directory, open ddraw.ini and set HiResMode to 1, Mode to 0, and SingleCore to 0
4. When the game launches, make sure you click "Yes" to disable the original HiRes patch in favor of Sfall's when prompted.

Note: The game might be unnecessarily heavy on the CPU. Be sure to take advantage of the Deck's TDP options and known Fallout 2 tweaks to remedy this.