If I create an Informix SSIS package in my 32 bit system using 32 bit Client SDK and deployed it in 64 bit server. Will it create issue?
You would need the 32-bit CSDK or Informix Connect (effectively the CSDK Runtime) on the 64-bit system (as well as a 64-bit CSDK or I-Connect for 64-bit applications). Apart from that, I believe that it should work. If it runs into problems, it is because of the Windows registry and the need for separate INFORMIXDIRs.
On 64-bit Unix systems, it was common to have both 32-bit and 64-bit versions of Informix CSDK or I-Connect on a single machine in separate INFORMIXDIRs. These days, there is less 32-bit code — there are no longer any 32-bit servers on 64-bit Unix systems, and usually there isn't a 32-bit CSDK either.