Should West read a low card as "not" discouraging in the following situation?
East doesn't know West has 5 hearts. If west had only AKxx and east had JTx, then continuing hearts would set up the third round for declarer. So discouraging from JTx, Jxx, or even JTxx (if opening leader could have AKx) is correct.

On this hand West should definitely continue hearts. It is safe, and given West's holdings in the minors, it's very unlikely that it's crucial to start an attack on another suit.

In general, saving your honors when they could be crucial for taking tricks is much more important than giving the right signal. Sometimes you have to trust partner to work it out without a signal. So don't signal with the Q from Qxx.

A couple more advanced notes:

This is indeed easier if you lead A from AK, since if the lead was from KQx or KQxx, you want to be able to encourage holding the jack.

Contrary to the previous answer, the situation when the lead is from AK and small cards are in dummy is actually one when standard carding does better than upside down, since with JTx you want to discourage but may not be able to afford an honor. This is a well-known position.