It probably does count, but it isn't clear how much. Defense seems to count much more than offense in war rankings to start with, so I can't imagine that improving a troop you can't use for much would be a big impact. No matter how many troops you have maxed, you are limited by the max troop space available. So if I were writing the weighting for this, it would have to have a balance that takes into account what the most powerful troops you have available are, and how many you can fit in the troop space. In that case, upgrading a second tier troop or tactic would make no difference if it weighs less then something you already have available. So upgrading a zeppelin mk3 to a bomber would make no difference if you already have strike fighters.
I don't know that Nexon has done it that way, but there has to be some balance to the limited troop space available. Every defensive upgrade obviously improves your defense without a tradeoff; every offensive upgrade is only an improvement relative to the options you already have.
Manifesto if I know I will NEVER use it, then I wouldn't waste the resources. But there are a lot of units that don't seem useful at first glance, but then end up being quite valuable with the right upgrade / university or library research / troop combination. So if I have already done all of the key upgrades in my armory, I will go ahead and do next tier things to give myself flexibility down the road. I know a number of people who left their factories and factory troops all at level 1/2 because they weren't interested in heavy tanks / global bazookas / armored car raiders. Then APCs and Tactical helicopters came along, and they had a long way to go to get to some really nice new units, as well as upgrades to bazookas and heavy tanks that substantially improve their usefulness.