I run mudguards with an alfine hub and horizontal dropouts. Just extend the back of the mudguard a bit further to give you clearance to get the wheel out..?
I’ve got a hilly commute (5-600m over about 24 miles daily) so can’t easily get away with SS. I’m never going back to deraileurs on a commuter it’s just shit and far too much faff. I’d also run a mile from cable discs or rim brakes.
My current bike is a Genesis day one drop bar with alfine 8, trp hylex hydraulics, microshift bar end shifters. I run schwalbe marathons and have full length mudguards. While there are ways it could be minorly improved it’s basically perfect and I’d buy another if I had to, over pretty much all other commuter bikes out there.