Don't worry too much about what I say (everyone has different opinions about everything), you are doing a good job, keep on making the game you want to make!
Here are some ideas to draw inspiration from for ? events:
1) Instead of % chances for things in choices, some could simply be "choose 1 out of 2/3/4 things to happen or none at all" with the player getting what they are choosing. They could also be simple tradeoffs (lose X, gain Z) or things that impact the future (right now, I will give you X, but later I will collect Z from you) or (I will give you X now, but the next fight or boss fight will contain Z, that will make it harder).
2) Item / inventory manipulation
2a) Welding / integration service: Welds one item in your inventory to your ship, making it impossible to move, but gives it a bonus of some kind.
2b) Crazy construction yard: Allows you to expand your inventory by 4 slots, but also installs 3 immovable 1x1 "support beam" -items in random places in your inventory.
2c) Item exchange, choose one: give 1 item, receive 1 random item of the same type. give 1 attack item, receive 1 random attack item. give 1 shield item, receive 1 random shield item.
2d) Makeshift modification station, choose one: Give 2 items, one will receive a negative modification, the other will receive a positive modification. Or: Give 1 item, it will randomly receive either a positive or a negative modification.
3) Special items that cannot be gained any other way
3a) Broken down ship: Give a consumable item (for repairs) and gain radar item, that makes every 5th click on the minesweeper open a cross-shaped area instead of just a single cell.
3b) Ship ran out of energy: Get an empty battery that you can charge during combat. Once it is full, the next ? event allows you to give it back and receive 'charge capacitor' item that charges up by 1 every time a nearby item is used and once it hits 5, the next item nearby gets triggered twice when it is used and the charges go back to 0 (with twice the effect, for example a shield would be "up to 20" instead of "up to 10" with this effect).
3c) Derelict ship about to be swallowed up by a black hole, you have time to scavenge 1 thing out of it: A malfunctioning phase-shield, that completely blocks every 5th shot against you. A powerful weapon that uses 5 energy per shot, dealing 50 damage (I compared this to the 35 I could do with 5 energy with the items I had), but also 5 damage to you (that cannot be blocked by shields). An energy generator that generates energy from enemy bullets, giving you 1 energy for every 3 shots taken against you. A gigantic missile, that will automatically destroy the first wave of ships (or just 1 ship) in the next battle you go in.
Some other ideas that came to my mind:
There could be more interaction between items and the mindsweeper map, as that is where most of the playing happens. Basically items with a action that does something in the mindsweeper area, also with no energy cost but with a cooldown or a "1 time per refreshed minesweep map" or "X times per battle" type of limitation.
Some effects that there could be:
1) A larger area covered on a click (such as with the radar).
2) Rapid searching: More clicks before enemies get energy.
3) Forceful excavation: Clears a large area in one go (say a diamond shaped 4x4), but only gain a maximum of 1 energy from that area, others are lost.
4) Efficient excavation: Finding an energy will give you X shield. Or finding an energy will 'ping' the area around the energy and reveal it.
5) Excavation drone: Reveals 1 random spot on the minesweeper map every X turns.
6) Rare mineral item (some item that uses a rare mineral instead of energy to use, with a very small storage capacity, maybe 1 or 2?): The item has it's own effect when activated, but having it will add a rare mineral to a random place in the minesweep map (1 per refresh?) that the player can find, but the map will still refresh after finding the energies, so it will not always be found.