Are there any explicit disadvantages in comparison to running it on a UNIX machine these days?
For one, it might not work at all. I tried recently(in April 2012) on two Windows machines (7 and 2008 R2), and some aspect of the PostgreSQL setup invariably fails.
I spoke to a Rapid7 account manager about it, and he confirmed that the Windows version is flaky.
He also recommended against using it in a production environment.
I have been using the Windows port of Metasploit for a while now and it is working great. Also, the development team have done a great job in packaging Metasploit for Windows, installing it is a breeze.
However, some Metasploit modules are not supported on the Windows platform, like sniffer ones (pSnuffle for example).
I had Metasploit 4.0 installed on my PC and it worked fine no issues. But, since i have reinstalled windows 7, it is now incapable of installing becuase of the PostgreSQL issue. I have MySQL installed. Maybe if Rapid7 gave us the option to use MySQL from install we wouldn't have this problem.
Also Metasploit fails to update on Backtrack 5 and a ton of modules do not work.