Ray's was never meant to reward stealth and theft skills.
What? He has dialogue acknowledging when you steal things and jets.
Styg clearly didn't originally intend for the place to be theft-proof—official acknowledgement that Ray's isn't theft-proof and that it's
possible to rob the place, however, isn't the same as deliberately intending that players rob the shop blind every playthrough.
I think that Styg intended Ray's to be very difficult to rob of jetskis and components, while the office is much easier to rob. Since his entire player base are grognards, it turned out that we had little to no trouble robbing Ray's of anything not nailed down. Hence, he's made it even harder, and finally impossible without turning the entire zone permanently hostile (and I disagree with him on that, by the way).
Rewarding Mercantile, however, was clearly very intentional. Ray's is THE premier reward for Mercantile now, other than secret inventories. There are minor dialogue trees related to haggling for every jetski, a Mercantile-based discount gradient for each, and the antique can be sold to him for a large sum with high Mercantile.
You say the existence of dialogue is proof that Ray's was meant to be robbed. While I acknowledge this, I say that Styg never intended the place to be robbed blind or for it to be a primary means of rewarding theft skills, which is borne out by his repeated attempts to stop it being robbed blind. The massively huge truckload of locked-away treasure seeded throughout the entire game is and always will be the primary means of rewarding subterfuge skills.