I am not familiar with the input encoding inside the GUI components. I believe that Swing simply uses whatever input encoding your platform is set to, so it should work when typed in and when displayed.
However, saving that information in external format and bringing it back in again is what I have been working on. So a token with umlauts entered in the Name field should AFAIK always work in MT as long as the campaign/token stays in memory. When written out and read back in, it may get screwed up.
Natha's comment about accented characters inside macro strings is a different problem. The GUI component which is the large text box should accept accented characters just fine, but the parser subroutine which is responsible for reading
that text is likely not encoding-agnostic.
Second, the German translation is embedded inside the MapTool JAR file. Anyone is welcome to extract the current file, make updates to it, and then send it to me for inclusion in the next build. (I have on my list to externalize the translations so they can be put into a directory instead, but that's more work and I'm into bug fixing right now.)
To extract the file you can right-click on the JAR file in most desktops and choose to "Extract..." as the JAR file is simply a ZIP file with a particular format. Note that making changes and storing those changes back into the JAR file may or may not work -- there is an internal structure that could get messed up when using a generic JAR utility.
Another possibility would be to visit the source code repository
and download the translation that you want to update. Note that the repository is likely to be even more up to date that the file embedded inside the JAR file.
If you do send me an updated translation, specify how you want your credit listed in the "credits" on the Help > About menu option. Although I typically will add people there after they've made 3-4 contributions, as just a single contribution would make the list pretty huge!