I assume that by Bostik you are referring to some sort of contact adhesive they make that would bond to the hypalon. If it is just a fill of silicone it is absolutely going to need mechanical removal. I have not had much luck using solvents on large silicone application "repairs". I have seen the joint between the floor seam and tubes filled with silicone before. It works, but is not repair friendly. With flexible silicone repair deposits I try to cut off as much as possible and then use a small sanding drum. The flexibility of a silicone caulk repair makes it a pain to remove with abrasive wheels.
Opened seams with just an original layer of old glue left over usually clean up pretty easily. If the former owner has layered on a two part glue it can be a real pain to prep (I found out the hard way). Glue does not bond well to old glue. On my PVC boat I found the larger abrasive wheel to be a bit too aggressive and hard to control. Dremel sells a softer smaller abrasive wheel that worked well for me and was easier to use in tight spaces.
Mek and acetone definitely soften up the glue and your boat material (hypalon or PVC). Thin layers of old glue may come right off, but thick glue really does need some mechanical removal. The abrasive wheel throws off a lot of the thick glue as small little balls of glue, thick glue will also advance in a line as you work across a section. Here is an image of thick deposit removal.
Ready for a rough rub with a terry cloth towel and acetone. Acetone flashes off faster than MEK and is better for light cleaning in that it doesn't soften the boat material as much.
I will pass along one tip that I have learned. When doing repairs there is often a seam that is not fully open or needs to be glued in sections. When you are applying the glue it takes longer for the glue to set to tacky in these crevices. If you wait for the tight edges to be ready the open areas can pick up haze. Lightly wiping the glued surfaces with a solvent/rag works, but even then you will often have glue that is still too wet in the edges of the repair. There will be a small little band where the glue isn't tacky enough to mechanically bond properly. Apply some direct pressure and the glue will cure. Without a little pressure you can get an incomplete seal or a weak seal in these edges, particularly when gluing floor seams these ends to the repair may leak at some point. I use a painters extendable pole for pressure in these shots.
A proper two part hypalon glue is the best way to go on all repairs for your boat. If the floor to tube material split isn't too big I would go for a hypalon top patch.