Unless you have encryption enabled it shouldn't create much of a difference, as Hamachi is only a medium for directing packets.
All network traffic (down to the ethernet layer) is wrapped, encrypted and transmitted through the tunnel Hamachi creates. The program must unwrap all the data, decrypt and supply it to the machine via the 'false' network adapter it creates, which can be a slight performance hit. There is indeed a performance hit since two players who can communicate directly between each other without the use of Hamachi have a lower lag than the same game being played via Hamachi.
As far as the encryption goes, it is enabled by default and you must be a 'premium' user to disable the encryption.
As for a tool like this, I am currently working on a Hamachi replacement type of program that is specific for Outpost 2. (Basically, it would use the SIGS / WON support layer built into the game. I would replace the SIGS DLLs which when present would normally allow the user to connect to SIGS, instead it would connect to a custom server, using a custom network protocol).
Basically it would be a small piece of software that allows people to arrange games. It would allow one person to create a game, and then other users could join the game through the software. Finally it would perform NAT punchthrough so game packets could directly travel between the clients in the game, instead of being 'tunneled' through some other protocol as Hamachi does.
Not only would this decrease lag for people but it would do away with some of the other inconveniences of Hamachi:
-- Hamachi has a 12 user limit per network, and users do not automatically leave the network when they exit the program, so we are forced to run bots to remove users on a periodic basis.
-- Hamachi must install a fake network adapter driver, limiting it to Windows 2000, XP, or better. This creates a whole host of problems since there can be some ambiguity when there are 'multiple network adapters.' For example, a server program started after Hamachi is running and active that binds to the first port available will often end up binding to the Hamachi IP, not the internet IP.
-- Security issues because Hamachi is a virtual LAN and other users could access files, printers, etc that are shared to the network if these services are not disabled for the Hamachi network adapter.
I have started work on a server and do work on it when I get the chance.