Rokets and Arillerie.

Railroad guns are good too, keeps you a longer distance away.

Remember that fortifications higher than level 3.5 will hide their contents from your view.

But if you do not know whether there are units in the inside, arty bombarding will just damage the fortifications?

You will see the presence or absence of units at close range, but they will only be shown as a ? and not any details such as type or number.

When I was new, I mistaken those ? units to be 1 infantry with low health and I was really wrong...

Use spies to sabotage
Use rockets (higher than level 2)
Be careful of artillery since if they are getting +80 you need like 5x as many as they have to make a dent
If they are not protected by AA or Patrols, Tac and strategic bombers will reduce the forts as well as units
Patience

Besiege them, like Vorlon said, with RRGs, or if you don't have those, arti. Put some melee units in front of the arti to protect it. This way, you force the enemy to either be stuck in their position and slowly be killed off or coming out and risk quick annihilation.
Very true. Never rush in a level 5 fort with just melee units. However, the enemy may have built that fort as a means of stalling, so don't overdo the troops, especially when you got the enemy cornered.