Experienced chemists can look at molecule diagrams and have an intuition as to its activity and similarity to other known molecules. It’s like most of science and math: most discoveries begin with intuition and are demonstrated rigorously afterwards. I believe Poincare said something to this end.

The brain is incredibly good at pattern matching while not necessarily being able to articulate why they came to that decision. Organic chemistry has these types of relations in spades. Say for example crystallization. You can kinda brute force it; there's only a few dozen realistic solvents to try, but that's a single solvent system. Then there's binary and ternary solvent systems. Then there's heat/cooling profiles, antisolvent addition, all kinds of things. Hundreds or thousands of possible experiments.

You might just decide that a compound "needs" isopropanol/acetone, plus a bit of water, cause something vaguely similar you encountered years ago crystallized well. You often start with some educated guesses and refine based on what you see.

But there's often no clear hypothesis, no single physical law the system obeys.