The perl libraries are compiled as 32 bit and FreeTDS libraries are compiled as 64 bit. Will this be an issue?

Yes, this will be an issue. as you can't mix 32- and 64-bit code in one program.

In other words, the executable (perl) and the libraries it uses (such as DBlib.so with its dependencies libsybdb.so.5.0.0, etc.) all need to be either 32-bit or 64-bit.

So, as you have a 32-bit perl (rather ancient, btw), you'd have to rebuild the FreeTDS libs as 32-bit.  The other option would be to build a new 64-bit perl (plus Sybase::DBlib and Sybase::CTlib), so you can link against the already existing 64-bit libsybdb.so.