How should you prepare towards an assigned rep which is going on vacation or won't be available for a while?

For the OOO period, the rep should mark his calendar as not free.
If the rep supports active chat, he should also mark himself as not available for live chat (Via My Account). You can also do that for him, go to Settings > Team & Roles > Click on his name, and turn off the toggle under 'Account Info'.

In the case where the rep is the only one assigned to a sequence, you can either turn off the sequence or add someone else to the sequence (Under Sequence's Settings).
You can also keep on sending emails, and schedule meetings for the rep, for once he comes back, whenever the OOO period is less than two weeks.

If the majority or entire team won't be available, and you would like to stop sending messages, you can just turn off the sequences for that period of time. In case someone replies back, the sequence's manager would receive an email notification for a new task that would be created. Then, once you're back, just increase the number back.

Have a nice vacation!