Mr. Campbell's plans (which represent the ship as built) do show four small air ports on each sie of the bow, the aftermost one in line with the center of the water closet and the foremost one just aft of, and below, the lower trailboard. They provided ventilation for the crew accommodations in the 'tween deck space. (There was a watertight iron bulkhead just forward of the forward hatch; on the 'tween deck level that bulkhead divided the cargo space from the forecastle accommodation space. The space ahead of the bulkhead below the lower deck was devoted to the bosun's stores and "fore peak store.")
When she was in Portuguese service, operating as a training ship, most of the 'tween deck space for the full length of the ship apparently was given over to berthing space for the naval cadets. At least a dozen more air ports were cut in each side, in a row running from the aforementioned forecastle bulkhead almost to the break of the poop. Those ports are still there - or were the last time I saw her, which was (I think) in 1997. (I suspect they'll get planked over by the time the big current restoration is finished. My recollection is that those ports are bigger than the old, original ones in the bow. Current photos should clarify all that.
Caveat: I'm assuming she got the additional air ports when she was under the Portuguese flag. She did, however, serve for at least a little while after that as a privately-owned British training vessel. I suppose it's possible that the ports were added during that period.
I ran across one interesting tidbit that may shed just a little light on the changes she underwent. It's from Mr. Campbell's book, China Tea Clippers, pp. 114-115. He's just been discussing the techniques for fabricating iron masts, which involved shoving a gadget called a "dolly" inside the mast while rivets were driven in to hold the various pieces of it together. Mr. Campbell continues:
" I recall an incident during the reconstruction of the Cutty Sark involving one of these dollies, with near-fatal results. One of the ship's masts [couldn't you tell us which one, Mr. Campbell?] , which had been a replacement after a dismasting, was found to be some feet [sheesh, couldn't you tell us how many?] too short, and in consequence I suggested adding the requisite lenth to the heel, thus avoiding altering the top and its cheek plates. This meant raising the mast by chain hoists inside the hold, seized around a heavy iron bar which passed thruogh two holes burned out of the mast. The mast had a full-length diaphragm plate as a stiffener, and a manhole was cut into the mast near the holes so that the diaphragm could be penetrated also. After the strain had been taken on the hoists, a shipwright put his head into the manhole to see if all was correct and as he withdrew it, a loud clatter was heard as a heavy iron dolly came hurtling downwards and bounced upwards again from the keel. It must have jammed inside near the masthead during construction and suddenly loosened with the vibration."
So at least one of the lower mast was shortened (by "some feet") at some time or other - and restored to its original length at about the time the ship went into her present berth. That story doesn't tell us anything specific about when the mast got shortened, but it suggests that looking carefully at the mast proportions in the Portuguese pictures would be a good idea.
Later edit: Shipwreck and I apparently were typing at the same time. He and I have similar questions about when the additional ports were added. It sounds like the shortened mast mentioned by Mr. Campbell might well date from 1916.