Upgrades - capacity controlled?
 

Simple question that I can't find an answer to: are suite upgrades, paid for with points from a deluxe-room rack rate (i.e. the 6,000 point for up to four days award), capacity controlled?

I don't know for sure, but since other awards are capacity controlled, I would assume so. You could ask CS. Or if you cannot book the upgrade, ask if you could pay for the suite at rack rate. If the answer is yes, then that would answer the question.

I just called and booked the upgrade in the end.

6,000 points to upgrade a four night stay at the Park Hyatt Tokyo to a Park Suite is an astonishing bargain, especially considering that the prevailing rate (49000¥ per night) was the only rate available other than hyatt.com.

Capacity Control
 

I was told there were no capacity control for utilising your points for an upgrade cert. Afterall, you are still paying a room rate, and I think that what counts with any hotel.
Award certs on the other hand are completely free, the hotel will not get anything from the guest, apart from the other on-spend charges.

Hotel will receive reimbursement from Hyatt GP, albeit at a very low rate based on hotel catagory.