Yeah, it's a 'problem' also encountered in other armies. My first question would be: Do your rules have the whole regiment acting as a single tactical unit? Or are they running around as individual squadrons? If they're all acting as one unit I'd just have one or two guidons in the 1st squadron. If they're tactically independent I'd have one guidon per squadron.
My Prussian SYW army only has one guidon per regiment of 16 figures - partly because more than one looks a little excessive but mainly because Old Glory only gave you two guidon-bearers in a pack of 31 figures (the 31st figure was a Garde du Korps eagle-bearer)…
When I did a load of 1806 Napoleonic Prussians in 'The Grand Manner' at 1:20 ratio I did each regiment with two guidons.
Is it possible to squeeze an extra figure on the base to add extra guidons? In game terms it won't count as an extra figure, but will look good... I've done this with Napoleonic and ACW infantry where they had more than one colour per regiment.