any experiences of this..?
Does being flatfooted have any detrimental side effects for the keen cyclist..?

not sure, I have them and the first shoes I used hurt my knees (main issue with having flat feet) I’ve used Spec BG shoes mostly until I got some 510 Minaars and I seem good with them.

I’ve got normal arches, but find (quite pronounced) insoles help my knees. I guess it’s a case of if somethings acheing then make small changes one at a time to relieve it. I’d guess flat footed-ness would be near the top of the list of problems to address if this was the case, maybe get a bike fitting at a place that does custom insoles and cleat wedges?