I think it's worth evaluating. Increasing their chance for success by 6.4% isn't that high a hurdle. IMO, it's a horse race against all the other next steps OP could take with his business. YC's a pretty strong horse in that race.
(I suspect there's also still room for negotiation, even if YC isn't advertising that fact any more. Three guys and an idea? 6% More than $10MM in revenue? Let's talk.)
The value of the business would instantly go up a lot more than 6% just by having "YC" forever attached to the company. All of the advising, connections etc would just be a cherry on top.
The value might go up by more than $600K right now, but assuming it gets to $100M, who knows if the value will have gone up by $6M due to the YC branding.
(I suspect there's also still room for negotiation, even if YC isn't advertising that fact any more. Three guys and an idea? 6% More than $10MM in revenue? Let's talk.)