Do people generally take out every warp gate adjacent to their claimed systems? Does the rank of the system with the warp gate affect the level of ships that can come through the gate? If so, then maybe it's only worth it to take out gates on level 3/4 systems.
If there's already a good discussion of this, just point me to it.
The easy way to look at it is:
Do you not want to have to defend against waves coming through that wormhole?
If not, destroy the warp gate.
The more complex way of looking at it is by examining the opportunity cost of destroying the gate. Assuming you have a set ceiling of progress you dont want to hit prior to taking out the AI homeworlds, you need to think about what else you could accomplish with that 10 progress vs spending it on taking out that gate.
Of course, this is also assuming you're not employing a "wave funnel" strategy, where you destroy or warp jam all entry points except for one. That's one way to do it, too.
The mk level of the planet with the gate does not affect anything besides the difficulty of destroying that particular gate.