The #1 reason for not defending the strats is it hurts your score. Your kill per hour will be in the toilet.
Unless you are explicitly going for fighter #1, you can still have a very good (top 10) fighter rank when you mostly defend the strats against bombers (think of the hit% boost)... that is, as long as you do good against the buffs
What made myself largely abandon the strat defense when flying a fighter was the breakup of the central strats. Traditionally there have always been less defenders than attackers, and most of the time I would be the only defender at all. So I couldn't simply cover them all, when I was here the enemy would strike there... and with a 180 min downtime and relatively small single factories, only 1 bomber needs to get through. Then add the often horrible locations, like directly in front of enemy bases, or other places where you actually can't see any bomber coming early enough... protecting the strats was suddenly getting mostly pointless in terms of gameplay.
I also greatly turned down my attacks on them, which (unknown to most) I was actually doing much more than defending them...