In a more traditional job, paid time off is a benefit that follows a strict procedure. Vacation days are accrued over time. Employees submit requests to their managers before they take these vacation days. These requests are explicitly approved or denied. When you take those vacation days, you leave the office behind and you fly off to Aruba without a care in the world. At least ideally.
When you are your own manager, it's hard to know whether to approve time off. Have you worked enough to accrue vacation days? Will the project get done on time without you? Is this a good time to leave or would it be better to wait and take a longer break later? When you do take time off, it's also more difficult to leave the work behind... the trade off of managing yourself is that the manager comes along on your vacation.
It's really important to take breaks away from work (and to leave behind the manager when you're off the clock). First of all, it's a chance to scale back from the nitty-gritty. It's easy to overemphasize the importance of the task you're hacking away at, whether that be a dissertation chapter or a set of documents or a stack of secondary readings on a particular topic. Leaving behind that tight focus for a few days provides a chance, upon your return, to reflect on the project as a whole. It's helpful to remember the relevance of that particular slice and to return to it with a renewed sense of purpose.
Perhaps even more importantly, vacation is a time to heal the body and mind. Writing a dissertation is an extreme mental workout! You have think deeply AND exercise an enormous amount of self control. Vacation is a break from harnessing willpower; it's a few days to be impulsive and spontaneous and lazy. Vacation is also a few days to stretch out the spine, rest the eyes, decaffeinate a bit (just a bit!), and maybe even expose the skin to sunshine.
I make a case for vacation in the interest of both the manager and the worker. Happy, well-rested graduate students produce more and better quality work. In summary, clocking out occasionally is an investment in the dissertation and not a detriment.