The only measurable difference will be velocity. The ¾” longer barrel will normally give you slightly higher velocities, so it‘s easier to make power factor. (unless you get one like mine that has a slow barrel)
Some (like me) prefer the longer sight radius and balance of the 5” model. Sights are no big deal as most shooters replace them by the end of the first year with something they like better. Much like your preferred drink, It doesn’t really mater, as long as it works for you.
Have you decided what division you want to play in? Most use a 9mm for Production division as it keeps ammo cost’s down. (everything gets scored as “minor” regardless of caliber) For Limited division, the 40 has a distinct points advantage. (major caliber)
Hope this helps.
Jeff