as for insects, the only insects you would need are pollinators. and they can be controlled. honeybees would be best but arent the only ones.
if you plan for the pop. to grow then you wont have as big a problem at the end. i assume that the animal life will increase over the time period as well.
Nuke subs also have the benefit of being able to surface every now and then to control air and water quality. You don't think they are underwater 24/7 365 days per year for decades do you?
Scrubbers only work for so long and certainly not for thousands of years.