2 Peter probably wasn't written by Peter and was probably written late first century to early second century. It's always been one of the disputed books in Church history.
But even ignoring that we have to remember that we have the benefit of cross checking all the various books of the New Testament against each other, while the writers weren't necessarily aware of each other's letters.
And even if 2 Peter was written by Peter and recognized Paul's letters as on the level of Scripture, there's no evidence that Paul considered his writings to be so. It would be against Paul's self deprecating character to self promote his own writings that way as being on par with Scripture and there is no indication in the NT that he does so; including 2 Timothy.
So on balance 2 Timothy 3.16-17 is referring to the OT (At the least, 2 Timothy certainly can't be referring to itself and including the letter of 2 Timothy itself as part of the sacred Scriptures to which it refers).
And regarding the common argument about the "worker due his wage," Paul can't be quoting Luke's gospel, because it probably didn't yet exist. Instead, Paul is most likely quoting a well-known oral tradition going back to Jesus; quoting Jesus's own words, which were obviously accepted as the words of the Lord, not because they are contained in a book but because the Lord Jesus said them. It's also possible to read it parenthetically as Scripture says "don't muzzle the ox" and the worker is worthy his wage.
Finally, even if we dismiss all my points above for sake of argument it still doesn't solve the problem that there is no inspired "Table of Contents" that accompanies Scripture to tell us for certain which writings the Scriptures are identifying as rubber-stamping as sacred Scriptures (if for sake of argument the above verses actually show this).
"All Scripture is God-breathed" but what does that include? Many second century Christians accepted works like 1 Enoch, and the Shepherd of Hermas, and the Didache. While other Christians rejected 2 Peter, and Jude, and Hebrews, and Revelation, and James (which no one even mentioned until the third century). The book of Jude and 2 Peter themselves also rely on and/or quote Jewish pseudopigrapha like 1 Enoch and the Ascension/Assumption of Moses. Jude quotes 1 Enoch as an example of end time prophetic fulfillment.
So, again, Scripture itself does not provide us with clear guidance regarding what constitutes Scripture (which is my overall point). We can only appeal to canonization outside of the Bible, which is equally debated and a matter of dispute.
BUT the good news is none of it obscures the Good News gospel message