My Apple Pencil 2 run out of charge completely, will it still be able to be charged?

You should still be able to charge it. It should not affect the battery condition significantly.

See this page for helpful tips for your battery:

Batteries - Maximizing Performance - Apple

Good luck!

Nothing I said contradicts what you said.

Letting it run out, and storing it that way is the danger.

And that is also explained in the article I linked:

"Do not fully charge or fully discharge your device’s battery — charge it to around 50%. If you store a device when its battery is fully discharged, the battery could fall into a deep discharge state, which renders it incapable of holding a charge. Conversely, if you store it fully charged for an extended period of time, the battery may lose some capacity, leading to shorter battery life."

Having have it run out does not mean it is damaged. But you should never store it an empty state.

So yeah the best practice is to avoid it, but it does not mean that it is damaged now.

The article you linked is NOT about Apple Pencil. Sorry, but the advice you offered is unfortunately not good advice for Apple Pencil, which has such a tiny battery that letting it become fully discharged can not only damage it, but can render it completely unusable and require replacement.

You have given the wrong information, letting an apple pencil drop to 0% will cause damage, and cause it not to work especially if you leave it before charging it again.

Apple Pencil, especially the 2nd generation are designed to be kept at 100% battery all the time.

You shouldn't allow your battery to run out of charge, it can damage it

In contrast to the post above, the pencil in Apple Pencil is teen tiny and should NEVER be permitted to discharge fully. If it is fully discharged for any period of time, it can die without the ability to be charged again. If that happens, if it is still under warranty, Apple will replace it. If it is out of warranty, you will have to buy a new one.

Bottom line. Keep your Apple Pencil charged and do NOT let it discharge. When not being used, it should be resting on the charging pad on the side of the iPad. This ensures it doesn't become discharged.