This is a set of old surnames I am interested in because of my wife's Flemish Boons (who I know have cousins in the US). When I first started looking at such surnames I came across all the typical theories, connecting all Boons to Bohuns. I have since seen a 16th century parish register which translated the surname into Latin for a bean, which is what boon means in Dutch. But I also remain open to the idea that the surname in this part of Europe comes from Bononia (Boulogne-sur-Mer, older Dutch Bonen) because I have seen in older records that Boon and Bonen, Boonen etc were often interchangeable. I doubt that these surnames come from Romance Bon or any old Frankish personal names, at least in this part of Europe.
I guess the bigger point to make is that any name which is a single easy-to-pronounce syllable is going to literally have one or more possible explanations in every language. The neutral hypothesis is thus that names with the basic form of Bo-n have NUMEROUS origins even if we restrict ourselves to the geographically small area around the English channel and north sea.