I don't know that Onyx does MORE than Disk Utility, in that specific area. What Onyx does is to aggregate all the "cleaning" functions one might need in one package, so that instead of having to do 10 things, I do one and end up with Onyx then triggering the 10 things. It's convenience. I'm also not sure that "clean deeper and more thorough" is accurate, either. When Onyx is invoked, it runs the same process as Disk Utility does in Verify (or that fsck does) and results in the same report. What the cleaning function does is clean out the logs, caches, temporary files, etc, that get cluttered over time. But you could do that by finding and deleting the logs, caches, etc, yourself, letting them get recreated by the system as it needs. But that's a pain to do, so Onyx does it more conveniently. But not more thoroughly than I COULD do (but certainly more thoroughly than I probably WOULD do, to be honest).
I recommend Onyx for two reasons: 1. It works, 2. It is free. When a user comes here with a problem that would probably benefit from Onyx, it's nice to have a solution that costs nothing. When we do have to recommend a solution that costs (ParagonNTFS, for example) many times the user asks if there is a free solution.
Again, as a business proposition, it's not a good idea to invest money (and time is money) into creating a product that is already being well provided by someone for free. If someone can add functionality, or speed, or some other benefit, then it may be possible to sell a product with a free competitor, but if the products are equal in utility, most folks will choose the free version.
In your GIMP example, the reason I didn't use GIMP was that the documentation was miserable and I couldn't find any books to tell me how to use it. For PhotoShop there were a ton of books I could get on how to become a power user of PS. Plus, given that I wanted to swap files with other users of PS, using GIMP and praying that the transfer of GIMP files to PS files would work correctly seemed risky. The same logic applies in Pages and Word. I got tired of people complaining that my exports from Pages didn't look right in Word, so I got Word, despite the cost. In those cases paying (or paying more) for a product that did the same thing was still of benefit to me because of the fact that I simply couldn't get the free or lower cost version to work for me.
But that logic doesn't transfer well to Onyx because it's so simple to use. The defaults are just about perfect and the developer has put warning messages where the consequences can be less than desirable. It's practically foolproof. I cannot think of any thing that could be added that I would be willing to pay for. However, if a developer tries it and actually adds sufficient value above and beyond what Onyx already does, then I might be tempted, if that value is of sufficient benefit to me.