Ive used two systems where this is a big issue, the Wii and the PSP.
Stories are similar between both systems - Sony would release a firmware update for the PSP, but usually within hours of release it would be released patched from the homebrew coders so that the public would be able to use the new features, while still being able to used the homebrew programs.
In a similar vein the Wii updates are released and then later cracked, however the recommendation for Wii updates is to stay at version 3.2 because it has the widest support for homebrew applications. The latest Wii firmware, v4, can be installed with patched IOS files, but if you upgrade to 4 on a virgin system you are pretty much going to have to wait until a hole is found to be exploited to again allow homebrew to be ran.
At the end of the day, it's your system, and you have to weigh up the benefits of homebrew to the benefits of the new features of the firmware update. It may well be that the updates dont affect the homebrew exploits at all, or it may be that the update forever patches that security hole.
To be honest, Ive never really thought to myself 'wow, that new firmware feature is something I must have and Im going to update right now', it does make a difference if features like the DSi shop or new games are blocked unless you upgrade, but to be safe I would suggest giving a little time to see what exactly has been updated, what on your system will be affected, and whether a patched update will be released soon to allow the best of both worlds.
The choice, as they say, is yours.