Is it THE reason? Hell, no. There are so many incredible mods out there that add so much to games that the improvement can be breathtaking. Fallout 4 with mods is my GOTG by a landslide. I have 100+ active mod files that together improve the game by leaps and bounds.
I've got a mod that lets me set custom damage settings, which is awesome (why don't games have this standard?). I have a mod that lets me add legendary effects to anything so I can use the gear that I like. I have one that gives names to generic NPCs. I have one that lets me buy DLC ammo without going to the DLC zones.
Anyone that tries to down-play all of that into "nude mods lol" is just being ignorant.
However, mods like Bodyslide (which is better than anything you see from game developers themselves) are amazing and the texture and mesh work modders do is first rate. I use Bodyslide because I love using different outfits and it's the perfect system for that.
Seriously, whenever you see people mention "nude mods", they usually really have no idea what they're actually talking about. Body replacers are generally used to improve terrible character models, improve customization, and to allow for the use to different gear (especially for fantasy games like Skyrim).