I am using nodebb-plugin-composer-default 4.3.2 and NodeBB v1.4.0.
The problem is present on Lavender and other themes. Looks like it is not related to the theme.
Category 1 had 17 topics and I 16 were deleted.
In home page you can still see total count 17.
Delete doesn't actually delete the topics, at the minute, NodeBB will only soft delete a topic. This was how it was originally designed, however, you can follow the progress on hard deleting topics here:
thanks @a_5mith I think you know more about NodeBB issues than I do at this point