I was recently replacing my rear brake pads, and I noticed that the caliper cylinder's dust cover was looking wavy, almost like it is warped...does this mean I should rebuild/replace the caliper or will it be ok since it isn't leaking at all? Thanks.

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Current cars:
2000 ML55 AMG, 174k miles
2003 C240 T-Modell, 202k miles
1995 S320, 207k Miles

If the Calipers are working OK and the Heat Shields are not getting in the way of something I do not see any problem.

There has been a couple of threads were people have rbuilt their own calipers and found the Heat Shields did not fit well. It could be a some point someone replaced them and force them it and caused the warpage.
But, they have been on your car and evidently have caused you no problems.

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84 300D, 82 Volvo 244Gl Diesel