I put Koni's on front and rear of my ACE 30.1 and noticed the same thing. The rear shocks don't have dust covers. I contacted Koni about is and they said that was intentional and being uncovered was not an issue because of their wiper system. Picture of one of my rear shocks is attached.
My chassis is a 2016 F53 and it looks like they eliminated the dust covers for clearance reasons. I first attempted to (incorrectly) use a front shock and found that there wasn't clearance for a dust cover. When I got the right shock, there was no problem. The uncovered section of the shock is pretty high up in the frame and I don't think much will get up there.
The OEM Bilstiens did have plastic dust covers but I didn't check if there was a clearance issue with them when I took them off. They are pretty narrow relative to the Koni's
I love the improvement made by the Koni's - no more porpoising when going over road dips, bridge expansion joints, etc, and way more control. I also put a SuperSteer rear Track Bar on at the same time I did the Koni's.
2017 ACE 30.1
2017 Jeep Cherokee Trailhawk