flat towing with a locker by itself poses no problem. Lockers are designed to unlock around corners when torque isn't present at the drive shaft....
The real question is usually around the tcase. Usually the question is 'Do the tcase bearings get lubed while flat towing?'. With a front disconnect axle, a locker will always spin the drive shaft (unless you have locking hubs). This can be bad if only part of the tcase is spinning and not the parts that splash the bearings with lube. The rear driveshaft will always be spinning too (unless equipped with full floating locking hubs).
The one way to ensure the tcase isn't spinning is to remove the driveshafts (or tie them away from the axle in the rear with the slip yoke). The lockers will not hurt a thing, and if anything, will help the Jeep track a little better on the open road.
-raymo
4.6 Stroker Scrambler