Having just two individuals of a species of social insect (such as ants, bees and termites) can be a problem. The male is often a drone whose sole purpose is to fertilize a queen. And the queen may be virtually unable to feed herself, being dependent on the workers. But if there is just one drone and one queen, there are no workers. And I think these are considered "unclean", so Noah could not use the "seven" exception for clean animals and birds to sneak in some workers. Presumably, then, each queen must start laying eggs immediately, to generate enough workers to support the colony. Now termites should be in good shape, because the Ark is made of wood, and most of the ants will be OK since there will be lots of detritus and food remains around. But I'm not sure where the social bees and wasps will get their nourishment, since all the flowers will be underwater for seven months.
But that suggest another problem to me. After the flood, all the terrestrial plantlife on the planet will be dead, having been indundated by saltwater for so long. Most of the animals on board depend on plants for food, and will starve before the earth can recover. Pretty tough to be fruitful and multiply when there is nothing to eat. And learning from Carthage, when the land has been salted, it can take much longer than normal to recover. Anyway, all those plants that have co-evolved with pollinating insects can't spread without the insects, and the insects can't thrive without the plants. Oops.