Hi Josef,
There are plenty of designs that had them launching from the top. There are some Northrop designs I've seen here that have them and I've seen many hypersonic designs that show them launching from the top to keep from interfering with the flow field to the inlets as you suggested. The Blackbird could have them on the bottom, because it's engines were out on the wings where the missiles wouldn't have much of an effect on them. I'm sure they studied the local flow field coming off the of the open doors of the weapons bays in that regard.
But now that I look at the drawing of what you are modeling, they would have opened on the bottom. Since they are to the side of the inlet, they wouldn't effect the flow field to them at high speeds. As Flateric noted, they're easier to access that way. Also, even with the extending launch rails, I would have been worried about them launching upward near the vertical tails. If they were going to launch those up, they would have been close to the centerline away from the vertical tails.