2.
If you are saying that a ship configured for auto-mining would not be as powerful as a ship set up for combat, I agree with that. You have to min-max your ship design for the role you want at the time. I would replace cargo holds with generators when I was about to take on a tough enemy.
If you are saying that the game needs to permanently make you decide between auto-mining and combat ability, I refute your idea vehemently. I should be able to obtain gear to max out my gathering AND my combat.
And besides, I am sure some people will still love mining in the end game, and so they should have the option to do that without any hindrance to their game. Make auto-harvesting and instant puzzle solving an option, and not a necessity. And by option, meaning that you aren't hamstringing yourself by not using the technology.
If you didn't want to auto-mine, you wouldn't have to purchase, obtain, or install the module.
Essentially, yes, an auto-mining or whatever specified ship should have gaping holes in other areas, as RPGs, even RPG-lites, require the player to make decisions on how s/he wishes to play, and the player shouldn't be capable of having an all-in-one ship, even at the end game. As for the auto-mine module, I am saying that not having the auto-mine module should not be a major hindrance to your game performance (as in, you should be able to make that decision on the merits of the system alone, and not hamper yourself just because you like the mining mini-game. It should be an option to play the game effectively, not a necessity). Even being optional module does not mean it wouldn't be "necessary" for maximum game efficiency, so to speak. For comparison it would be like having an insta-gib and OHK anything weapon in a game like, say Fallout 4, with an easily achievable price point. You should be able to acquire that weapon if you don't like combat, but it should require a significant time and economic commitment to acquire it, usually at the cost of some other area.
To sum, I am fine with an auto-mine module as long as it isn't so obviously superior to manually mining and requires a significant resource investment to acquire. Don't want to mine? That is fine, but it will be achieved at the cost of lower combat capability, at least initially when you would be able to acquire the system (in the late, late, late game if players just refuse to end the game, you should be able to plug-and-play the system with a more combat-oriented play-style at will, but that would be at the point when you have acquired essentially all technologies and a practically infinite source of RU).
An auto-mine mechanism could be balanced in a number of ways, most obviously as follows...
1. Costs a ton (as it should)
2. Acquires less resources than manually grinding all the resources off the planet (so you don't have access to infinite resources once you buy it, otherwise that would make this module a "necessity" in terms of game balance)
3. Takes up a large space for a module (kind of like the Chmmr bomb in SCII, takes up a large space, but not all of it)
4. A little bit of everything
Preferred choice, not too excessive to make the module useless, but not too little moderation to make the module over powering.