A barrage of missiles does wonders removing pesky forts. Since missiles may only be fired to attack and may not be repositioned, you will have to build silos close to the action until you can build ground-breaker or supernova warheads. They have long legs and, if based in a central territory, can reach nearly the whole map. While this is expensive, it's worthwhile because deflector and especially anti-matter forts mow down tanks and troops like a combine harvester does wheat. Contrary to the documentation, planes can be shot at by anyone, though SAM troopers have a much better chance than others to shoot them down.
Forts are also very good at taking out aircraft, yet another reason to use missiles.
If it weren't for stacking limits, though, there wouldn't be much point in building them. When attacking a province full of colonists and forts you will have to over-stack to ensure victory. If you want to give the extras a chance to survive, set their withdrawal percentage to 50Don't be fooled by the battle replay into thinking you could have won and stayed within the stacking restrictions. The difference between sending in enough force and not enough will often result in nearly everyone making it or no survivors. Unless you need to, don't build ships.