I've had experiences both ways - Aquatic, Nexus, Seacam, Subal. If the handles are sturdy enough, they are fine there. If not, on the housing. The main point is the arm configuration is such to allow strobe placement where you want it, when you want it. One of my big gripes with camera housing designs is the ergonomics of the handles. Sea & Sea and Nexus are good, Aquatica's are better. Seacam and Subal, what the hell are you thinking?
Seacam handles work well for me (both with and without gloves). The outside curvature is particularly comfortable (fit in my palms). I have not used Aquatica style grips. The strobe mounting on the Seacam housing body, BTW which is on a thickened metal base, dictated my vote in the poll. I suppose one could attach a large tray to the bottom of the housing and add strobes ala Nikonos.
Too wide a set-up, however, is problematic for verticals. BTW, there is a rotating tray for Subal film housings from ULCS. This may be problematic for dSLRs because of the need to see the back. 