Does doing sysprep too many times cause issues?

Sysprep limitations are due to the windows activation process (and it's hardcoded limitations). To quote the manual:

There is no limit to the number of times that the Sysprep command can run on a computer. However, the clock for Windows Product Activation begins its countdown the first time Windows starts. You can use the sysprep /generalize command to reset Windows Product Activation a maximum of three times. After the third time that you run the sysprep /generalize command, the clock can no longer be reset.

And...

If you anticipate running the Sysprep command multiple times on a single computer, you must use the SkipRearm setting in the Microsoft-Windows-Security-Licensing-SPP component to postpone resetting the activation clock. Because you can reset the activation clock only three times, if you run the Sysprep command multiple times on a computer, you might run out of activation clock resets. We recommend that you use the SkipRearm setting if you plan on running the Sysprep command multiple times on a computer.

Assuming you are using a KMS: We recommend that KMS clients use the sysprep /generalize command where the value of the SkipRearm setting is equal to 1. After capturing this image, use the sysprep /generalize command, where the value of the SkipRearm setting is equal to 0.

Just curious, if you are deploying through SCCM, why not deploy from OS source and apply patches during your install? It takes longer to configure your initial tasks, but in the end run the whole process is greatly simplified and the maintenance is extremely easy to handle.

I'm far from a Windows admin, but as far as I'm aware there are no issues sysprep'ing a machine as many times as you want.

There is/was a limit on how many times sysprep can reset Windows Product Activation's clock (IIRC it's 3 times though so if you've already run sysprep more times than that you're probably fine :-)