Some early dictionaries did in fact do this, and this was also the case with Roget’s project with his thesaurus (most contemporary thesauri arrange the main headings in alphabetical order, thus the title, “Roget’s Thesaurus in Dictionary Form”) where he arranged the words in a tree of classifications.
Most rhyming dictionaries are still alphabetical, but I think it was Webster’s that kept a file of headwords alphabetized in reverse order (so order would be sorted as redro, reverse as esrever, etc.) to facilitate the creation of rhyming dictionaries, but a case could be made that this order could be useful on its own.
Isn't this what enciclopedias are? You have animals in one section, you have countries in another, you have every component in a motor vehicle in another, etc.
Perhaps encyclopaedia is not the word. As a kid I had tons of book like this. I still remember one of my favourites had a whole section on what I believe was housing temperature control and insulation!
Most rhyming dictionaries are still alphabetical, but I think it was Webster’s that kept a file of headwords alphabetized in reverse order (so order would be sorted as redro, reverse as esrever, etc.) to facilitate the creation of rhyming dictionaries, but a case could be made that this order could be useful on its own.