Yes, I think that's it. https://codeberg.org/FoxSylv/Verbose-Engineering/src/branch/main/utilities/createDecompilationRecipes.lua#L31 sets unlock_results=false for most decompilation recipes, which means that unlocking uranium decompiling does not unlock the 2,3,5,8 digits.
The letter decompilation recipes do set unlock_results=true (which is default), and each letter can decompile to itself, so all letters are unlocked items as soon as you research letter decompiling, as well as 2 from decompiling Z. But unlocking uranium-238 decompiling does not unlock 3,8; digits only get unlocked once you have a non-decompilation recipe that produces them, such as number addition.
I don't see any reason why decompiling should use unlock_results=false; removing that should fix the problem for 3,5,8. It does get the slightly weird situation that unlocking uranium processing unlocks 3,5,8 but not the other digits, but that shouldn't be a real problem (you legitimately cannot reach the other numbers yet at this point); it's just a UI peculiarity.