I'll preface by saying I don't really care if people like mods or not. I sometimes use them. I mostly don't.
I think any dev trying to fight mods though is fighting a losing battle. If a game gets popular enough people WILL find a way to mod it.
Not sure why devs would waste time on shit like that...
I can think of two reasons that make sense to me. Whether they are good reasons is debatable.
1. Devs may intend for you to play a certain way.
2. Devs may be concerned about reputation and trying to control potential damage to it.
Mods can undermine the intended way of playing a game. If the dev wanted certain things to be in the game then they'd have probably put them in themselves. It's something you used to see triple A's complain about. I think it's always been rare to see indies dislike mods though, indies tend to want people to keep their game in people's mouths and modding communities are as good as any to be talking about your stuff.
As for the reputation thing, I have seen someone in the past point to examples of malicious shit stuffed into mods and unofficial ports that blew back onto the original devs as though it was there all along. Some people are actually dumb enough to install a shit load of mods and then think the malware or whatever was there all along. And then some other people are dumb enough to believe word-of-mouth that
x dev puts viruses in their games.
There are probably other reasons but those are the two that I immediately thought about.
