More than likely they'll install to the same locations, so yes there could be problems if you try to install the same modules different ways.

Pros and cons would be:

• Using the OS' package management would give you an uninstall mechanism
• It may be slightly easier to use the OS' package manager to install the same set of packages on large numbers of machines
• You're likely to get more timely updates to packages going straight from CPAN (i.e. you're at SuSE's mercy waiting on them to package a new release; or you'll have to roll your own local package)
• You're likely to get a wider selection of modules straight from CPAN (you may need Some::Obscure::Module that isn't going to be packaged because there's 7 people on the planet using it)

There's probably more, but that gives you some sort of an idea. It's similar to any other "use OS' package management" versus "compile from source myself" decision.

Update: Very good followup below by Anonymonk, especially the one about compilerless boxen.

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