I hate when my boots make a clicking noise! j/k
did they replace the inner tie rods? if those are worn it may start making some noise.
the BOOT is not going to make noise, or produce a "clicking feeling" come on, a rubber boot???
next time you take your car in for squeaky brakes, they will say its the tire.......
anyway, without driving it or looking at it in person, its hard to know whats going on with it. Maybe its too minor to bother with, but I still do not buy that its a boot....