Hi, thanks for your comments and inputs. The shop behaviour is not meant to add difficulty or influence progress. The idea is to give players more useful options instead of stuff that is not fitting the current build at all, which is very frustrating and was one of the most brought up issues in earlier versions. The feature should help the player and make the fitting of the ships more satisfying. It's simply buggy at this point and makes the process even more frustrating instead. I'm aware of that and I'm working on it to fix it.
I'll put out an update fixing this and the weird ship behaviour you are mentioning asap. That's another new bug, making the experience a bit frustrating in this version.
The behaviour of the popup box can be influenced by tapping the health bar. It makes the box disappear and decides if the box pops up on selecting a ship or not. I'll change the default setting to it not popping up and add a tutorial step for it, so players are aware of this feature.