I think there already exists strategies for dealing with assassins. They aren't invisible, for one, and they are weaker, so you should be able to take them down assuming equal numbers if you attack them first, rather than hoping to win on defense. Mages can go for earth mana to have stone-skin; it'll take more than one assassin to take down a stone-skin mage in a city, probably 2-3. If you see a large stack, hit them with collateral damage units, so the assassins are weak enough to lose out. Use your own assassins, you should have mobility advantage in your own lands. Etc.
If it is the fact that it seems odd to field large numbers of them, remember these are abstractions and the assassins could represent special forces type units who might be fielded in large numbers in a war (and each unit is much smaller than a unit of champions, that's why they lose on defense).