I reckon the system already caters to targeting external and main systems, as Might = Hull; Speed = Engines; and Intellect = systems inc weapons. So to target specifically engines, weapons etc that is easy. Increase the difficulty of the shot and the damage goes straight to those areas, (- shields etc).
But I would also like to do a GM Intrusion/Major Effect table where other internal systems, inc all the upgrades, weapons etc can be hit/damaged accidentally too. You know - where the lights go out, the antigrav inside stuffs up, Hyperdrive hit, scanners down etc.
BTW: Absolutely no need to make up PC-style stats for really big craft, unless the PCs come to be in charge of one. Like PCs, only player starships are created this way.
NPC ones are like NPCs from the core book. They get a level (which determines DCs and health), then you simply modify up or down (in level) for sepcific areas), such as a level 4 light freighter (level 6 for shields, level 6 for hull) to represent mods. Of course you could base these mods on the Upgrades or even abilities listed for PC ships.
(Might want to look into how PCs and NPCs/monsters differ in this sytem - one of the parts I LOVE as creating creatures etc are a breeze).
You're right about the Excel. I wouldn't use it UNLESS you kept it up to date with ALL the Descriptors and Foci I have on the charts on this site. Hence why I keep them. If people kept these Excel things up to date I might use them, but given the VERY few starships that I will ever create, I would just use up to date charts on here, as again, it is only for PC ships.