1 always has to be to achieve a political aim through fear, otherwise they're not really terrorists ;)
Now I want to understand them
1- why are they doing it?
2- how they are getting funding?
3- where they keep the ships and why imperial security can't track these easily?
4- do population supports them, if yes to what degree (what if they are usurpers or radicals or some sick sect no sane person supports)?
5- how they call themselves?
1- your empire is occupying another state, who wants their independence back.
2- individual freedom fighters using their own personal resources.
3- they're private ships until the moment they're used for an attack (revealing the owner).
4- there's many sympathisers against the occupation, but not publicly because no one supports the killing.
5- (occupied state)-freedom/liberation/democratic/republican-forces/army/league... Etc...
1- your governance is seen to be at odds with individual freedom, leading to rebellion.
2- Foreign anti-empire enemies use their intelligence services to make contact with cells of sympathisers and to covertly smuggle funds/assets/training, or overtly provide aid packages to areas under attack by your anti-rebellion forces.
3- They're innocent ships that have been hijacked - hijacking airliners has always been a powerful terrorism trope.
Or, They're your ships, stolen from your bases that were reached by the rebellion.
4- it's hard to tell. All the universe's media is only publishing propaganda. There's support on both sides, split largely by geography (distance to your capital/strongholds).
5- The general people's congress, the transitional council, (season/landmark)-(peoples) e.g. sovereign-square martyrs.
1- Your say: because they hate freedom, they're a death cult, they're murderous madmen. Really: because they give you an excuse to weild an iron fist. Whenever there's unrest at home or your popularity drops, have your secret police blow up a Cafe housing some of the rabble raisers (while blaming the terrorists). Two birds with one stone!
2- the 'black income' of your own intelligence services. Drug running, extortion, etc...
If your own government has no transparency, then you can find them directly.
3- inside your own secret internal security bases. The anti-terror squads are lower ranking than internal security.
4- you run honeypot operations, having security pose as supporters to find actual supporters, so you can send them to the gulags.
The citizenry just wants their local Cafe to stop being nail-bombed, so they support any action you make.
5- you give them an Emmanuel Goldstein like figurehead for people to direct their hatred at, and give the group a foreign name similar to an actual enemy culture, to encourage nationalism.