I realize that this is sometimes useful, and so removing it as an option is, strictly speaking, a slight nerf to energy-weapon-using ships. I just think it's an awkward mechanic, and it is pretty useless most of the time - so simplifying things a bit by removing it is worthwhile.
It is pretty much useless for all shot-based weapons.
However, it can be
EXTREMELY (I cannot stress it enough) useful to beam weapons - just because you need that few points of damage to break enemy ship's flux dissipation and start building up his flux. Best example? High Intensity Laser - some may say it's not worth anything, but it has low OP cost, very good range, and low flux. You can stay out of Dominator's range all the time, and slowly build up his flux, thanks to increasing your damage via F key (provided you have two HILs of course - one is still not enough).
Regardless of ship attacked, ability to increase your damage output is very valuable when used with beam weapons - it essentialy helps overcome their biggest problem which is soft flux buildup. It doesn't make a tactical laser an anti-capital weapon, but it gets you the edge needed. While exposing you to an overload, of course.
That is my opinion on the subject, and while I understand this decision, I do not agree with it.