"There are 23068 users active, 200 of whom are invisible."
A non-defining relative clause with "of which" and "of whom" after quantifiers or numbers can be interpreted in this way. The above sentence containing a relative cause can be rewritten as:
"There are 23068 users active. 200 of them are invisible."
The phrase of whom defines the function of selecting a particular quantity in itself, hence there is no need whatsoever of using the extra word 'out'. It is uncommon, but not unheard of. However it means the same as the former expression 'of whom'.
Even GoogleNgram has very low entries of 'out of whom'.
Now your third sentence uses the phrase out of [anything] at the beginning. This structure is heard of. It would mean, from within their group there are three who didn't show up. It is actually similar to the previous sentences.
You can slightly reframe the sentence to mean and convey the same thing:
Out of the expected people in this group, 3 of them didn't show up/turn up.
But at the same time you can also write this sentence in terms of the above mentioned phrase.
There are 10 people in this group, 3 of whom didn't show up.