Most LAN capable applications are useable over Hamachi. However, there are external limitations that can make some not useable over the connection.
The application might not be optimized for data transfer over a non-LAN connection. Since you are always ultimately limited by your Internet connection itself, this can always be a factor in any application used over Hamachi as compared to over a physical LAN.
You may be exhausting either your upload or download bandwidth. Over utilizing your Internet connection on either end will have an impact on the other. For instance, peer to peer file sharing, streaming media, gaming, or hosting web services on your connection will impact both upload and download capabilities. This will appear as slow ping times, slow file transfers, lagged streaming media, lagged/dropped game connections, or sometimes even slow connections or the inability to connect to the Hamachi mediation server.
Performance is always limited to the maximum speed of your Internet connection.