I've played with the area-defense guns mounted vertically, but you trade better flank coverage for worse dorsal coverage. I'm imagining that this ship would, in most engagements, be stunting wildly, and it's probably easier to have the dorsal face be the optimal arc. That would mask the fighter bay as well, and possibly allow for easier and safer combat launches. Better then perhaps to keep a few dedicated guns ventral, and have most of the gun armament dorsal.
As for ion cannon, I was thinking: the Customs Corvette, which is about as interception oriented as you can get, has no ion weaponry at all. The Sienar Guardian and system patrol craft small boats don't either, and barely carry a boarding outfit to boot. Live fire to disable? It might be a simple trade off given a reduced power budget; to carry enough ion cannon to make a difference against ships, you compromise the rest of the armament and the resultant need for more mounts and more guns thus push the overall cost or space/power use past what is easy to accommodate on small utility hulls. This ship I envision as being more an all-purpose light fleet ship, so scouting, escort, anti fighter and anti-corvette sweeps, and patrol would be emphasized over customs duties (it might well be able to do the latter, but might be a bit overkill, and the lack of ion cannon doesn't seem to disturb Imperial Customs so much, given the ships in their OOB).
As for missile armaments; I'm fairly torn. I suppose it is a way for small combatants to punch above their own weight by power generation, but against point defense, what use is a small missile salvo? In a space-limited design, you'd want as much dual- or multi-purpose weaponry as possible. Keeping heavy warheads that might or might not ever be used doesn't seem very good for that, and would be a hard sell for a design meant to be produced in massive numbers, as most small ships would be. If you really need missiles, it might be best to load an air group that will carry them more flexibly anyway (and, in a sense, are the ultimate multi-purpose weapon for small combatants).
It raises an interesting question about missile armaments in general in SW; you don't see much of them as capital weapons. The VSDI was obviously a missile boat, but the VSDII dispensed with them for what was supposedly a more ship-to-ship oriented design. Venators and Acclamators had a very small possible missile volley. Executors supposedly had a lot of concussion tubes if you believe WEG, but you don't see them being used, and in a ship that big and expensive you can pretty much mount whatever you damn well please, even if you just felt like being perverse
ISDs aren't really thought of has having significant missile armament. It might just be that turbolasers are that much more cost-effective and flexible.