Of course you can use modules. There's no difference between code you write and code you take from CPAN as far as Perl is concerned. There are a number of pure-perl modules that implement strong 2-way encryption, like Crypt::Blowfish_PP.
Comment on Re: Encryption using perl core functions only
I don't have strict.pm or warnings.pm on the embedded platform, but I could remove those pragmas from the module and inline it with my program. There are no dependencies for Crypt::Blowfish_PP too which is nice. Thanks for the pointer, most of the encryption modules I have looked at on CPAN have an XS component and I didn't want to attempt those on the embedded platform.