Can water based polyurethane be used to prevent knots in pine wood from bleeding through white paint?
Shellac is usually applied to knots prior to top coating. I've not heard of a absolutely foolproof method of sealing knots so that will stop potential bleeding from occurring. If you do decide to paint, then you have more options for addressing bleed through if it occurs. 

I think it's also worth pointing out that if you decide to paint over the finished wood, you will need to prep. That means sanding in preparation for painting. That's difficult work when your surface is overhead on a ceiling. My advice would be to finish a small section and temporarily mounting it on to the ceiling so you can decide whether or not you like the look before you decide on just finishing or painting the wood.