Basic trigonometry won't work as the ships wouldn't be in visual range. You're forgetting these ships are supposed to be no bigger than the stem of the base. You can't use basic trigonometry if you can't see the ship because of distance and your advanced targeting computers/sensors can't get a fix on the ship to determine distance. Even if you can see the enemy ship, there's really nothing to use as a point of reference to judge distance in space, so you are back to best guess and needing a deviation roll.
You do bring up a good point though, against ships without stealth it's not as big of a deal if they don't deviate.
What I'd really like to see is that you have to make a stealth check to use energy mines on ships with stealth (using the lowest stealth rating of all ships in range), unless there is another ship without stealth in range of the template or you've achieved a targeting lock on at least one of the ships with stealth that is within range of the template. This would satisfy my dislike of the energy mines as they stand, as you've now got something to use for targeting data.