At the start of the war in Europe, I selected to not product munitions for my european companies so that I could apply for military contracts but then it just shut's down my factories due to the war.
So I thought, maybe it's because my HQ is in North America, so I wait until Nov 1941 for when the US enters, and again I select to close branches, keep factories, and to not produce munitions. But everytime it shut's down all my factories and branches automatically and so I can't actually apply for contracts due to no factories available.

When a foreign country goes into full war, the game halts all consumer sales and terminates all contracts within that country.

When your HQ country goes to war, the game halts all consumer sales and terminates any civilian contracts within that country.

All factories in full war cities are closed with one exception.

You can bid on and use your factories in your HQ country to fill military contracts for your HQ Country. So in your case, you can only bid on contracts for the United States military, and your factories within the United States will only work with United States military contracts.

If you do munitions, you can not do contracts. And the only time you can adjust it is with the Action Memo popup that occurs when a factory location has a change in war status.

Another problem is during the war I like to purchase bankrupt companies to secure more factories. However, I noticed that all of them are being used for munitions, but none of revenue or expenses made from the newly acquired companies are going to me. I was hoping that acquiring their factories would mean they're making money for me.

If memory serves me, the game switches their factories to whatever setting you have. So if you selected for your company not to do munitions, they'll stop doing munitions as well. Reason being is that munitions production increase the risk of factory loss and has a negative impact on image ratings. But I am not sure this is the case, so I will double check it the next round of bug fixes.

And is there a quicker way to close branches? My hand gets tired clicking every single war once the war starts because they're still eating funds after I've idled all branches.

Use the districting system in the world map.

https://www.youtube.com/watch?v=iLTH9fWYmx0