*technically there are multi-hex weapons out there.
Starbases give 'boosts' to ships in their zone (when upgraded).
an ideology choice gives a free escort fighter to any freighter in your influence zone.
...
as examples.
I get the annoyance wrt single transports wandering around looking for an undefended planet to snipe. The AI does seem to like doing that, though never tries to protect them.
ofc the other side to than annoyance is that no matter the military levels or planet defense levels, or size of population, a single pop-transport can take out a planet 100% of the time.
If invasions were cleaned up and fixed, the single transport issue wouldn't be much of an issue.