Hi & welcome to the forums!
1. Is installing SMSQL at a later point in time an available option or will we need to install it now so it knows how the files are laid out originally?
Installing SMSQL later will be perfectly fine - no issues with that.
2. Obviously from a Windows perspective a 3rd party windows defragmentation tool (Diskeeper) will be useful, but from a SAN standpoint will it cause too much I\O and be detrimental?
I recommend you don't use any host-side defragmentation tools - or use them very sporadically, being conscious of likely outcome. Host-side defrag in most cases will balloon your existing snapshots, as from filer point of view all moved blocks have been changed, so it's not a very desired result.
Running reallocate command on the filer side may be advised though. There are some thoughts around this:
http://communities.netapp.com/message/20969#20969
http://communities.netapp.com/message/12493#12493
Regards,
Radek