HSN is for products / commodities. SaaS companies (service providers) will have to use SAC codes.
Anyway, these are just technicalities.
SaaS company should ideally fall under 997331:
997331 - Licensing services for the right to use computer software and databases.
If you're registered under service tax, you'll already have this (your SAC code).
This code won't change once you transition to GST.
Hope this helps!