I have split a large text file into a number of sets of smaller ones for performance testing that i\'m doing. There are a number of directories like this:
/h
From the information provided, it sounds like this would be a completely straightforward translation of your C# idea.
for i in /home/brianly/output-*; do for j in "$i/"*.[0-9][0-9]; do ./myexecutable -i "$j" -o "$j.processed" done done