Thanks for your reply. Actually, after posting my message I decided to buy a license just because I felt unfair to not give back to the developers of such a wonderful tool. Although probably my experience will not improve much with the paid version.
Also, I would probably agree with those who think that investing time in developing a fancy graphical interface is not a good decision. In reality what I am lacking the most is a good visual cue which could easily tell me that the file I’m looking at is linked to something else (I know the menubar icon can do that but I don’t find it very effective).
The fact that hookmark works under the hood is a double edged sword: In my case, I usually forget that I have linked one document with other resources, so by instinct I navigate to those other documents manually instead of simply using hookmark. Which is the whole point of having this app!