Protecting Virtualized SSIS and SSRS servers
We are using Veeam to backup our sql db, ssis and ssrs servers.  We are using native storage snapshot integration, which makes them happen faster.  Still we have some issues when running a snapshot when an SSIS package is running.  I would advise avoiding running snapshots during your SSIS package runs.  

SSIS and SSRS encryption keys are stored on the machine and don't rely on any externals, so a restore of an entire machine will not require an additional key restore, although it is a good idea to back up your keys in case you have to rebuild and manually restore a machine for some reason.  

We still run sql backups of all of our databases including ssis catalog to a network share.  We are planning to use Veaam for those 'application level' backups in the future.