I have been thinking about a workaround for the inability to create units that break up:
Why not designate the ship's bow as, for instance, a mast or ventilation duct in the S3ditor zones property tree? While modding SH3 I designated pieces of deck cargo as "masts", with no ill effect.
For instance, masts are designated as "type 15"; just create half a ship as the parent object and then import the bow, designating it "type 15" in the editor and maneuvering it into the right place.
This would have the added benefit of making it possible for a ship to lose its bow without being destroyed, as was the case on certain occasions (see, for instance, the attack on "Esso Nashville" in 1942):
http://uboat.net/allies/merchants/ships/1461.html