All other things being equal, in Starmade, the bigger ship will win. It does not take long for people to figure this out. A player with a modicum of tactical sense and a great deal of free time can in a matter of days, bootstrap themselves into flying a titan scale brick of system blocks, barely concealed with an unwedged layer of hull blocks. They then think they 'rule' and some will wish to lord their putative 'skill' over other players. To those who have not been able to invest so much time, these can indeed be intimidating.
Fortunately however, things are NOT equal. Those enormous bricks are ridiculously vulnerable to well thought out weapon systems on fleets of smaller ships. I currently have a million blocks worth of such smaller ships (25, 4000 mass destroyers) in a fleet around my homebase. I challenge any of those ten million block 'titans' to come visit and take a pot shot at something.
Prior to being able to build such a fleet, a player is advised to make use of their home station's invulnerability. Build an enclosure on your homebase that holds your undeathenator, build block, factories, storage, etc., so you cannot be astronaut killed while doing stuff. They cannot cloak their giant ship, you will be able to know when they are in your system. If they are, simply hide in your station till they get bored and leave. For the most part, you will simply be left alone.
It is possible they might leave attack drones in your system. Again, you will see them. Make sure to put at least a couple of weapon systems on your homebase large enough to do damage to such drones (my homebase has 24 capital ship turrets at this point). If they do leave attack drones around your homebase, given time, they will be destroyed by your invulnerable homebase weapons. Log on, tab out, watch a movie, come back.
The reality is that the only players that get 'griefed' that way are those that have not weaponized their homebase. For drones they might leave elsewhere in your system, treat them just as you would a pirate station. Don't go near it till you are ready to kill it. Mine elsewhere.