In an older version ctrtool 0004003000009802.cia --contents=Content worked. (Namely 0.7.)
Now it requires an option like -v or -q (or some other) and it needs to be in a different order:
ctrtool -q --contents=Content 0004003000009802.cia
Would be nice if the old syntax worked again. Output of the tool doesn't really matter to me but previously it did output way less. So it might be nice to have a non-verbose default output?