When Kovri comes out will a 3 letter agency see if I am running it?
It depends on where they're listening, but yes in the sense you probably mean.
The I2P protocol underlying Kovri has a signature like any other protocol, and anybody who can see all of your traffic can see that you're using I2P. I don't think I2P even tries to make that hard at all... and if it did there would still be limits to what it could do against a sophisticated adversary.
Corporate firewalls, ISP traffic statistics and quality of service equipment, and the like can also detect that you're using I2P if they care to look for it.
Like Tor, I2P mostly tries to hide what you're doing, rather than hiding that you're doing anything.
The short answer is yes.
If you connect to the rest of the I2P network (Kovri is a way to do that), some government organizations will undoubtedly be running a node that will attempt to log your IP. They will not know what you are using I2P for (that's the whole point of I2P), but they will know you are running I2P in the first place.
If you run I2P withing Tor, your service will be very slow and government agencies will know you are using Tor, but they probably won't know you are using I2P. I can't really think of a good case where you would want to do this in a reasonable setting.
Part of the reason Kovri is beneficial for I2P also is that Monero nodes will also run I2P nodes, which adds more users and more legitimate uses to the I2P network. Currently, a very large portion of I2P is used for Vuze traffic.
TL;DR: they can see that you are using I2P, but they can't see what you're using it for.