@VG, while waiting for Michael to comment this is my humble opinion.
Having build guitars myself I'd say that they are a mix of a mechanical and organic object. Thus one could say there isn't a right or wrong answer to this.
However, as I'm sure you're already aware of, if you think in terms of a "subtraction" process (removing material from a wood blank), I think it's more in favor
of NURBS modelling rather than polygonal. Routing a body and the various pockets (booleans), beveling the edges (fillets), constructing a neck with "profile" gauges (loft), all terms very similar to what one is used when working with MOI.
I'd say stick with MOI, because you are already producing awesome results!

My 2 cents.

PS: sorry if my wording seems a bit strange, English is not my native language.