Here's just a thought about mine-spam, and I don't know if the programming is past the point for this to be even considered but...
Eliminate all individually placed mines, and use the following abstract system which could hopefully add levels of strategy, depth, and won't paralyze your computer at the same time...
1) Instead of using Tactical Slots, could a New slot be added to the planet developement window "Mine Defenses".
Perhaps Mine Defenses can only be purchased after some Research has been conducted.
Allow different levels of mine Defenses per planet, possiby for example, TEC 3 upgrades per planet, Advent 2, Vasari 1, or whatever.
Mine Defenses can have a random chance of damaging each ship every X second time interval.
Chance of damage/Amount of damage/other effects can all be affected by the levels of research conducted. (See #3 below)
2) Allow the upgrade only to be purchased when a minelayer is present in system, and/or if possible, minelayer needs to be present throughout the length of the upgrade.
3) Consider adding additional researches regarding effectiveness of mines, or special effects or something.
4) If you have a fleet with a Minelayer and/or scout in system where mines are present, then you are "immune" to mine effects. Maybe requiring 1 scout per level of mines developed at the planet. If you are in a fleet battle and the enemy takes out your mine protection, then you'll be vulnerable.
Or implement some other Ability to protect from mine damage and set on autocast, minimal Antimatter cost, or always in use unless interrupted. Give various Ranges of "Protection" for each ship, small range for a scout, very large for a minesweeper. (Also affected by Research).
5) Add the ability for a Minelayer/scout to Remove Levels of emplaced mines at a planet, and/or prevent new contruction of mines, implement like sort of an Embargo against mines.
No, this solution doesn't cover mining areas with no planets, but Mines only work in system where they can be controlled so they don't blow up your automated trade ships or refinery ships, or <insert whatever other explanation you choose>
Feedback? Thoughts? Bullets?