There is a backwards compatibility:
Connectors Windows files SAP transport (data extraction)
SQL connector 6.3.1 6.1.1 or later
BEx connector 6.3.1 6.1.2 or later
Query connector 6.3.1 5.80 SR2 or later
Report connector 6.3.1 5.80 SR2 or later
Extractor connector 6.3.1 5.80 SR2 or later
BAPI connector 6.3.1 5.80 SR2 or later
So if you are using the Windows files of 6.3.1 you cannot use the SQL and BEx connector against the 5.9 SAP transports. I would recommend to import the 6.3.1 transports if possible. Or upgrade to the latest version 6.5.1. On the Qlik download site there is a Release Notes summary document where you can read about improvements and bug fixes that have occurred after 6.3.1.
That depends on which connector you are using for the transfer of SAP data.
QlikView SAP Connector 6.3.1 will only talk to SAP systems that have transports that are no older than 6.1.1 (SQL Connector), 6.1.2 (BEX Connector) or 5.80SR2 (all others). Many Connectors don't even need transports. Check the release notes for further details.
As Kaushik already explained, it's best to keep all installations in sync, and take the opportunity to upgrade all SAP Connectors and installations to the latest version (6.50) with the added advantage of important bug fixes (especially 6.3.2) for some connectors. If you cannot upgrade them all, use the transports of v6.3.1 and plan an upgrade of the 5.90 system.