Ygtjki

It sounds a little odd, but trying to understand if that's the recommended way to communicate.

E.g. 9900
"Nine-thousand-nine-hundred"
vs
"Niner-thousand-niner-hundred"

In the UK, the RT rules for the ANO are in Cap 413 and section 2.13.2 states:

All numbers used in the transmission of altitude, height, cloud
height, visibility and runway visual range information which contain
whole hundreds and whole thousands shall be transmitted by pronouncing
each digit in the number of hundreds or thousands followed by the word
HUNDRED or TOUSAND as appropriate. Combinations of thousands and whole
hundreds shall be transmitted by pronouncing each digit in the number
of thousands followed by the word TOUSAND and the number of hundreds
followed by the word HUNDRED; examples of this convention are as
follows:

Table 5 
Number Transmitted as Pronounced as 
10 One Zero WUN ZERO
100 One Hundred WUN HUN DRED 
2 500 Two Thousand Five Hundred TOO TOUSAND FIFE HUNDRED 
11 000 One One Thousand WUN WUN TOUSAND 
25 000 Two Five Thousand TOO FIFE TOUSAND

There isn't a specific example of NINER here, but given that the examples do actually use their prescribed pronounciations, you'd expect NINER to be used too.

I can't remember hearing it but the other conventions seem to be adhered to by professional pilots in the UK (we Sunday afternoon bimblers are not as good at it). Non-native english speakers are very exact in their use of the published pronounciation

No doubt there will be a professional along in a minute, who can give you a more authoritative answer

EDIT: The reason I can't remember hearing "Niner-thousand-niner-hundred" may be because, in the UK, it would be above the transition level?

Several numbers are not pronounced the way they are in English. Niner is the most obvious and most US pilots use it. In my experience, tree and fife are heard less often. I don’t recall ever hearing anyone say fower.

From Wikipedia

The NATO phonetic alphabet, officially denoted as the International
Radiotelephony Spelling Alphabet, and also commonly known as the ICAO
phonetic alphabet, and in a variation also known officially as the ITU
phonetic alphabet and figure code, is the most widely used
radiotelephone spelling alphabet.

ATC should always use the correct pronunciation and phraseology. Pilots aren't as consistent, at least if they're native English speakers; as long as we're understood (the primary goal of communication), we can get away with a lot of shortcuts.

In the US, NINER THOUSAND is used by most pilots, but you'll hear NINE occasionally. NINER HUNDRED doesn't come up often since we usually fly at multiples of 500 feet, but I'd expect the same tendency when it does.

I've never noticed US pilots using TREE, FOWER, FIFE or TOUSAND, though. Unlike NINER, those aren't easily distinguished unless you're listening for them specifically. They seem to be used mainly by pilots whose native languages don't have the sounds necessary for the normal English versions.

NINER is an artifact of the "phwa phwa phwa bwa bwa what-the-hell-did-he-say" days of radio telephony, with vacuum tube equipment and carbon microphones and raspy, garbled, muffled audio, to prevent it from being mistaken for the number five.

With the FM radio quality audio of modern avionics, it's not really required any more and sometimes you hear it and sometimes you don't. No controller will scold you for saying nine instead of niner.