Two reasons to use the updated customer keys:
1. Sage Aatrix
2. Sage Advisor
Apparently if you don't use the new keys when you install Sage 100 ERP 2013 then these two items won't work. Probably not an issue immediately though many customers suddenly want to start using Aatrix and it will be a pain to swap and test keys mid-stream during busy time.
I know when I did the last few rounds of upgrades I generally used the old keys.
On this next round of Sage 100 ERP 2013 we should grab the new ones which also means that we'll want to take a list of what's registered before and after the new keys go in (and a copy of the old keys)