The ark was designed to be moderately self-sustaining but it's not a totally closed system. Over time supplies of vital resources will run low. They, for example, use lithium filters to remove excess CO2 from the air, which can't be replenished. They simply bring lots of them with them, more than they will ever conceivably need.
It went without saying that, in the long run, the Cloud Ark as a whole was going to have to be self-sustaining in terms of food production. Water would have to be recycled. Carbon dioxide exhaled by humans would have to be used to sustain plants, which would produce oxygen for the humans to breathe and food for them to eat.
Preserving mass is practically a religion for some of the inhabitants, but it's made clear that they do have plenty of leftover mass (presumably including all of the ingredients found in a human) to spare and aren't averse to using it when they absolutely need to.
“We’re dumping mass,” Sean said, nodding. “As soon as the Cloud Ark runs out of propellant, it loses the ability to do all of the things that make it a viable architecture for long-term survival. It becomes a big sitting duck.”
He let them roll that around in their heads for a bit, then went on:
“Mind you, almost everything else that we do up here can be done with
minimal effect on mass balance. We can recycle our urine to make
drinking water and our poo to make fertilizer. Very few of our
activities involve just releasing mass into space in a way that we
can’t get it back. This is the exception. I have been ranting and
raving about this ever since the idea of the Cloud Ark was announced.
So far all I get in return, from the powers that be, are vague answers
and hand-wavy happy talk.”
Bodies are pretty much the only exception to their rule. 5000 years worth of bodies (assuming a static population of 2000 and an average life expectancy of 50 years) would contain about the same amount of water as a few Olympic-sized swimming pools, a not insignificant amount, but hardly a big deal when you're using that much or more as reaction mass each time you do a minor course correction. Water and the majority elements in a human body are relatively abundant on the Ark in any case.
Ivy made a unilateral decision that they would carve out an exception to that new policy. The deceased were moved into an empty orbital module docked at the truss. This was left open to space, so that freeze-drying of the bodies could happen out of sight and out of mind. When it filled up with dead people, they would have some kind of ceremony, the thing would be deorbited, and they would watch in silence as it drew a white-hot streak across the atmosphere below.