Hmmm ... so the button to attack the territory has disappeared or when you click to attack, does the progress bar move, but when it reaches completion nothing happens?
If the second, it could be this issue: http://www.gog.com/en/forum/castles_series/technical_issues_with_castles_2/page1
Eventually we decided it was "save on quit" causing the bug, but saving manually in the game allowed it to work.
If the first ... so when you click on an enemy or neutrally controlled territory what do you see? Do you see spy, scout, merchant, saboteur, and attack (for an enemy territory) and scout/attack for a neutral territory? Or all of those options but without attack? How many soldiers do you have? Are your military command points full doing something else? I think you need at least 2 free military command points to dedicate to an attack - if you don't have enough, I believe the button does disappear. Also if you "police realm" or something with the army, you can only use the military for as many tasks as you have task bars. You start out with only one task bar, so the military can only be used for one thing at a time at first (though you can use some of its command points for political/management tasks). If the military is already doing something, again the option to attack will disappear. As you gain command points, eventually you gain a task bar so you can do two military actions at once. But again, if the military is already doing two things, the option to attack will disappear.