On command points and moving on

"When both players exhausted their direct activations, the indirect activations phase starts." Sorry if this is obvious to others but do both players need to use all the command tokens before moving on to indirect activations? The Japanese order "All hands on deck" implies that no, since you can use command tokens for repairs.
Which opens another can of worms: Players Tom and Jones have the same amount of command tokens. Tom had taken he initiative so after his turn he has 1 and Jones has 2 tokens. Jones uses one of his tokens to shoot and ends his turn. Tom wants to use his last token during the repair roll. Since Jon still has command tokens left and it is Tom's turn, is Tom forced to use his last token or can he decide not to, letting Jon have two turns in a row?

Hello Crispico, and welcome to the Naval War forum!

To answer your questions:
You are correct that you do not have to spend all your order tokens in the activations phase. It is even advised to save some for other orders later in the turn.

Your opponent can keep playing activations after you have passed. Only if the second player also passes the phase ends.

In the 1.5 rulebook I've added the following text:
"Running out of activations
When one player has no more activations he wants to perform, the other player may continue playing activations. If both players pass for an activation, the phase ends. However, it is allowed to activate with a tactical order token even if you passed activations before. Still, once both players pass, the phase ends."

Note that tactical orders are a new feature added in 1.5

I hope this helps!