It's funny that you bring this up. I had a need to use v3 of the API to avoid IE browser warnings with maps on secured pages. I made code changes to use maps API v3 and submitted them to Joe. The changes are in the source repository now and will be in the next release of mojoPortal.
The only caveat is that if you choose the option to use "Local Search" in a Google map instance, it will fall back to v1 of the library, since local search is deprecated and has been removed from v3.
Jamie