Simple really, a lot of missions of higher rank aren't any more difficult they just pay more for no apparent reason.
Make them harder, add NPCs that hunt you (and who are actually any degree of successful in interdiction) to high rank data delivery missions, make high rank pirate massacre missions spawn wings or larger more dangerous ships that start hunting you partway through the mission instead of just adding more sidewinders to grind through...
I agree. Tougher NPC opponents, more likelihood of mission wrinkle(s), more non-combat challenge in achieving your goal, having missions automatically require multiple steps to complete (I don't mean follow ons).
A few examples-a very high paid black box salvage mission could have the added difficulty of (a) legal, non-hostile "claim jumpers" trying to get the black box before you, (b) the black box might be spawned within a dense debris field, or within an asteroid field/ring, within the exclusion zone of a military CQC asset, or just inside the orbital cruise limit of a planetary surface....to name a few.
A data or cargo delivery might be made more difficult by a requirement to *not* get scanned even once, or the need to meet with a 3rd party to either recieve the haulage, receive instructions on delivery location or hand off the haulage.....or it could be a combo of "don't get scanned" & "3rd party contact".
Planetary scans should be in ever larger Proc. Gen. Facilities, requiring significant searching to find the data point, or you should have to scan multiple data points to unlock the one you need, or the facility should be hostile towards your scan attempts.....or a combo of all of the above.
Surface salvage missions could also be made tougher by the presence of more and/or tougher skimmers, the pressnce of 1 or 2 Goliaths....or even a small ship...or the salvage could be in a hard to reach location and/or very well hidden.
The hostile ships might be sent against you warning needs to be much more of a sure thing too.