I finished the quest Those! and after talking to Dr Lesko he ran to the nest. I read that it's a bug that he can dissapear after that, will that affect any quest later?

As fas as i know hes only needed for that quest, although he has a unique lab coat if you kill him.

Ok, well I just read that you can sell ant nectar to him, hope he's still there

After the quest is over, I've found him in his shack in Grayditch.

You don't have to kill him for the lab coat. Just complete the optional part of the quest successfully. You can make serious cash selling nectar to him.

Yes, you can sell Fire Ant Nectar to him as a source of caps.

The fire ants in the metro respawn for me. But I'm running FWE and MMM, I'm not sure if they respawn without mods.