In Sanctum (tower defence) you get the most damage for your money by building low level turrets. However, depending on how you build your maze not all turret positions will be equal, some will be able to shoot for long periods of time, others not so much, so the optimal strategy would be to build high level towers at the best points, low level towers at the lesser points, and nothing at the very worst points.
RTS games are quite different, the whole position aspect doesn't exist for mobile units. A typical formula is to make the high level units overall better for their price, but make it so that you have to do an initial investment in order to be able to build them, that could be do some research that takes time and cost money, or build a structure to enable the construction. So the player will have to balance when to move for the higher level units, which at that point will decrease the immediate unit output and thus temporarily weaken the player. Another thing to do is make the strengths of the units different rather than one just being stronger than another, they will have different perks making a strategy that combines them and is capable of adjusting depending on what the enemy does optimal. This is for instance very typical for Blizzard RTS games, but it takes a lot of skill, time and testing to do just right.
And finally an anecdote:
The optimal multiplayer strategy in the RTS game Earth 2150 is to choose the Lunar faction and build nothing but Lunars equipped with machine guns. This is basically the cheapest fighting capable unit in the game, whenever taking fire it's gone almost instantly. But it's cheap, and very quickly produced, so you can field an abundance before the opponent has a chance to do anything serious.
Not a lot of people ever discovered this on their own, everyone just presume that it's a worthless unit, because that is what a lot of other games and campaign mode has taught them.
Balancing is a really tough job, and it's very easy to fail in anticipating a simple winning strategy.