I have read, in a book about the Ho 229, that the airfoil choice was made because of the wooden wings and the difficulty of keeping laminar flow in service. I do not know if this is accurate or not, but I suspect not, as from an engineering & manufacturing viewpoint I do not see why they would have thought it was more difficult with wooden wings than metal (if that is what was meant, but maybe they were referring to maintenance issues?). From my viewpoint I suspect that they actually just kept it simple since the 34°-35° swept wing would allow the aircraft to reach its critical Mach number of ~M.85 without getting fancy.
The NACA 2414 airfoil has a critical Mach number of M.8-M.85 when combined with the sweep angle, so it should have done the job just fine.