After playing through a modded version of the game for some time I realized that the difficulty, even while set on nightmare, was far too low. I was one shotting enemies even while naked. The mods I had installed were Combat Tweaks, Improved Atmosphere and handful of cosmetic and QoL improvements that I doubt would have effected the difficulty.
After failing to get the increased difficulty optional file for Combat Tweaks to work (the .gda one) I decided to just reinstall the game, delete the Bioware folder in My Documents and try all over again. I saved my character folder so I wouldn't lose my playthrough progress. Unfortunately, when I loaded the vanilla version of the game I was still one shotting bad guys, while naked nonetheless. My override folder is empty now and I have no clue what could be wrong.
TL/DR: The difficulty is too easy, even on nightmare, and nothing I do will increase it. Enemies die to one or two hits and a reinstall didn't fix the problem.
Any advice would be appreciated.