I was taught to pronounce the oo in either afternoon or noon as /u:/ ~~the oo in nook~~ until I found some native speakers pronounce the noon sounding like new-n (videos). But the AmE IPA in the dictionary labels it as /nu:n/, instead of what I thought it as /nju:n/ if it's pronounced new-n. To my surprise, the IPA of new is /nu:/ rather than /nju:/. If /u:/ is equivalent to /ju:/, so why the word moon, whose IPA is /mu:n/, is not pronounced as mew-n?
In much of the U.S., /u:/ and /ju:/ have merged after /t/, /d/, and /n/.
That means if you pronounce noon as /nju:n/, people will still understand you, and probably won't even notice you're pronouncing it differently than they do. I don't know if I've heard people use /ju:/ after /n/, but I've definitely heard it after /d/ and /t/. This is generally called yod-dropping, which would imply that the /j/ is dropped, but it might be more useful to think of it as a merger, as there are some people who pronounce both due and do (when it's stressed( as /dju:/.
On the other hand, these two phonemes have only merged after some consonants, and not after others like /m/, /p/, /b/, /f/, /k/, and /h/; if you pronounce moon as /mju:n/, you're much less likely to be understood; in fact the two words moot /mu:t/ and mute /mju:t/ are distinguished by the /j/, and if you say “it's a mute issue,” it's not clear you'll be understood.
Finally, the 'oo' is nook is a different phoneme than is in either mute or moot.
I was taught to pronounce the oo in either afternoon or noon as the oo in nook
That was poor teaching - it is wrong.
noon, n.Brit. /nuːn/; U.S. /nun/;
moon, n.Brit. /muːn/; U.S. /mun/
nook, n. Brit. /nʊk/, U.S. /nʊk/ (some dialects pronounce as /nuːk/ particularly parts of Scotland - but this is non-standard.)
until I found native speakers pronounce the noon sounding like new-n.
[Newn] is non-standard or dialect - you need to say where these "native speakers" are from.
The "y" sound ([j]) found in "new" - nyew - is know as the intrusive y and is a feature of English.