Yes, user-made high resolution textures ruin games. Wait, usually the opposite of that.
When I'm playing primitive 3D games, particularly the 1st generation of playstation & saturn games & PC games up to the late 90's, I sometimes get confused. Why does the lampost talk? Why am I shooting carrots? Why can't I drive over the other ramps I'm racing against? Which way did the perspective go again?
Anything that improves the visuals can improve the experience. Visuals don't make the game, but they're a part. There's always a place for nostalgia in playing a childhood game, or preserving the original as time wears on cartridges, but for just "playing a game" improving it is an improvement.
That said, some texture packs show as the texture artist's first project. Like turning up the sharpness and saturation on an old video can help, but really cranking it makes a noisy mess. If it's worse, it's not an improvement, but a learning experience. Sometimes a mod can disguise itself as only the HD texturepack, where the artist's style clashed with the original work, and for a fan of the original game, the new pack can just look wrong. Texturepacks for N64 have gone well.
For me personally, I'll feel nostalgic and disable HD temporarily. Otherwise, the retro/cellshaded/fun packs are joyous. For playing through, if the artist has stayed true to the original vision, where the gameworld looks as if the main character had forgotten to wear glasses before, HD texture packs are literally brilliant.