I notice a lot of Skyrim mods do this, particularly those that focus on adding content to the world. One example is the otherwise excellent Expanded Towns and Villages, http://skyrim.nexusmods.com/downloads/file.php?id=13608 by missjennabee.

Just wondering if it's no longer an issue like it was with Oblivion?

It's still an issue. Mods should NOT be deleting refs.

I delete refs on the daily. Did me good. I don't even crash anymore because of it. How, you ask? That's a good question. I like your style, kid.

Because now my save can't even run at all. So... no more crashes.

Cave Johnson here. The lab boys are telling me that it was not a good idea to delete those two million refs in order to build our multiverse total conversion mod. Someone's gonna have to go back, undo all of that and disable the refs instead. Good news is, Greg made us a java applet that's going to do all of that and make our plugin as healthy as an aurochs again. Or, so he said, before we fired him and downloaded TESVSnip. Signing out.