Were there two Black Neuroi Hives?
Yes, there's another Black Neuroi Hive that was destroyed at the beginning of Strike Witches 2.
According to a more general question asking the total number of hives on Yahoo! Chiebukuro (Japanese), which was answered by mr_hungry01:

The new hive that occurred at the beginning of season 2, episode 1 is right above Venezia facing the Adriatic Sea.
At the same time, the destroyed hive was displayed on the screen as if it was on the city facing the sea, but in setting it is said to be &quot;Hive of the South Karlsland&quot;. Together with the fact that the 504th use this strategy against Neuroi crossing the Alps mountains until it was destroyed, it seems it's around in the inland north of the Alps mountains.
 (partial answer focusing on the 2nd season only, emphasis mine)

The Wikia also mentions this:

As of 1945, Neuroi hives have been confirmed in the following regions.

[...]
South Karlsland - apparently located near the Rhine river, destroyed by a stronger hive that later established itself in Venezia;
[...]