Well, there’s been long standing speculation of direct German and Austrian involvement in the Balkan wars. Specifically, the Slovenes and the Croats were armed by Austrian and German equipment, even during the so-called arms embargo which seemed to apply only the Serbs and Muslims.
However, what specific interests Germans would have in Kosovo, now, after the whole mess... I’d be at a loss as to what their purpose/interest would be. Seems to me they’d have a vested interest in the whole place (Balkans) being as quiet and as calm as can possibly be, as they have other issues to deal with (economic crisis, resurgent Russia...)
Who knows. One thing I will say is that the Balkans is a conspiracy theory central. Everything that can be imagined about anything in the world generally is imagined down there.
And is quite often true. This is largely because the Balkans has been used as Europe's chessboard for centuries. Everybody from the Turks to the Germans to even the French have screwed around in Balkan politics.
When it come to Germany, think Drang Nach Osten -- The Drive Eastward-- tried WWI, WWII and in the 1990's. Originally, Poland & Czechoslovakia were the targets, but the Balkans proved much less protected and more vulnerable.
There are German fingerprints all over the destruction of Yugoslavia, including the faked BND report that was used as an excuse for the 1999 NATO Bombing.
Germany blamed Serbia for WWI and its aftermath in Germany. WWII, Germany bombed the crap out of Belgrade in Operation Punishment, one of the first terror bombings of the war and it killed thousands. But Operation Punishment and Serb resistance cost Germany precious time, delaying Operation Barbarossa into Russia, and this is what cost Germany the war. (I also recall reading, during the 1999 NATO Bombing of Yugoslavia, that one of the NATO pilots was the grandson of one of the Luftwaffe pilots who had bombed Belgrade in 1941.)
Lots of bad blood between Germany and Serbia, going back nearly a century -- and Germans are not exactly the forgiving type.