I have a Ubuntu 11.04 installation and I use it for a local Subversion repository. Since 11.04 is no longer supported, I am going to upgrade to a supported release soon, and if possible to the latest version. If I upgrade, will my Subversion data be hidden or lost in some way?
It's a good thing you are trying to upgrade to a supported release. Upgrades should run without issues as package maintainers are doing quite good at handling this. Also, packages should not touch user data directories. However, as is valid for all valuable data, make sure you have a backup!
Concerning Subversion repositories, you should have to worry about incompatibilities either, as 1.6.x is packages from Natty 11.04 until Quantal 12.10. Only if you decide to upgrade to 1.7 you should be diving into upgrade scenarios.