Tejon is correct. When you remove a mod there is
absolutely no guarantee that your savegame will even be playable afterward, much less "clean." The fact that you can get away with it so often is a testament to careful mod design and pure dumb luck.
Case in point: if you save a game while a mod-added magic item is active on a target, and then reload the game without that mod, the item will have disappeared. The actual effects of the magic - altered stats, summoned creatures, etc. -
remain permanently.
There is an exception, though. When a savegame is loaded, the engine will recalculate the 'Max' component of the player's actor values. This is the component affected by some magic effects (Fortify,Drain,Paralysis,Feather,etc) from some kinds of magic items (Potions, Poisons, Enchantments, Spells, Powers, Lesser Powers, and Diseases). Any combination of those effects and magic items that is active only on the player is safe to remove.
Abilities behave differently (they affect the Base AV component), so mod-added Abilities are
not safe to remove. Other kinds of effects (e.g. summons or script effects) are not safe to remove. And
nothing is safe to remove if it is active on someone or something other than the player.
@ABO - in principle, you are right. Information on Active Effects (including their magnitudes) is stored in the savegame. Unfortunately, there is not
enough information for the game to accurately reverse "orphaned" active effects, so it simply ignores them. One of my goals with the Oblivion Magic Extender is to address this problem, which will render this entire thread moot. But that's for the future