The limit is per sector, so you can put 100 mines in every single sector of a given system.
The main use for units (that is, fighters, with possibly some drones thrown in for good measure) is when you have a rather long period of peace, allowing you to build a host of such units without any maintenance. But in such cases, you should either go for big or stay home, as one or two hundred fighters won't do much against even a moderate fleet.
However, the main problem of units is to strike the enemy, since fighters cannot warp and drones aren't the most versatile hull around. So good luck for sending these fighters against an enemy fleet when warp openers are running. Now if Warp Openers are not available, a few thousand fighters would make for a very nice taskforce for your defence.
Mines might remain useful even in the endgame, if you use them to bother your foe by putting them in his systems for example. If Warp Openers are disabled, you might also use them to make scouting your systems harder, requiring a minesweeper just to reach the other side of the wormhole alive. Or in short, an opportunity may arise for you to use mines, but you shouldn't hope them to do much good to repel this fleet of three hundred warships currently heading for your homeworld.
[ May 30, 2004, 09:56: Message edited by: Alneyan ]