I think Belle's baby belongs to Philip because I can't (for the life of me) recall Belle and Shawn being intimate enough for the baby to be Shawn's. When they were together, they were going to wait til they got married, so the intimacy would be special; however, they could've decided to have 'relations.'
Time will tell...soon enough. Something w/take place or a DNA will have to be done, and the proof will come out then.