CPAs: just fine.
They either attack your empire essentially everywhere, allowing you to respond with your mobile fleet and defeat it in detail (though outlying fabs will most likely be lost), or form up into a carrier hammer, allowing you time to prepare (build turrets/lightning warheads) on the single world (always the closest) that they will attack. Either way, this is not supposed to be an easy or routine thing to deal with, and they embody that difficulty very well.
As for defending fabricators, no, it is not possible to ensure their safety to anything close to 100% against a cpa. And it shouldn't be.
That said, losing a fabricator is not a big deal. You can still use the special ships when it really counts (the HW attacks), just not in your everyday fleet. Same for advanced factories.
Exos: also fine.
Fabricators/advanced factories are almost impossible to defend, but you have other ways to boost your mobile strength (whatever was causing the exo in the first place).
Warp jammers: already important, they should not ensure complete safety or anything close. To really defend a planet, you need turrets or fortresses, regardless of military command mark or miniforts.
Drifter defence: military IIIs and miniforts should beat a small (<100) threat fleet, or a dark spire spawn. Anything heavier should crack the system.
In conclusion: I see no major imbalances in player defences.