Recently we had one of our younger batters (16) padded up for 2 and half hours during a long partnership. It was a hot day and the youngster sat still during the partnership and then when a wicket fell, was unfortunately out first ball

What advice or tips can you offer younger batters when they’re waiting a long time to bat?

All batters are different as they wait for a wicket to fall and it's their turn to bat. Some are chatting, some quiet, some fidgety and some like to keep still.
Batters need to work out as quickly as they can what works for them. A long partnership can make it easy to relax and become too comfortable and just as you do a wicket falls and you’re out in the middle.
The young batter you mentioned is only 16 and they’re probably not used to waiting around so long to bat. I’d encourage them to be proactive every 20 minutes or so.
Standing up and walking around for 30 or 40 seconds to keep their legs moving and perhaps doing a stretch or two. Even shadow bat 2 or 3 shots to keep the mind and muscle memory active.
Very important not to be sitting in the sun, find shade and a comfortable seat.
The old saying one wicket brings two rings true after a long partnership so the batter coming in needs to be awake and ready to go.

Every couple of hours let someone else take your spot for 10 minutes, take the pads off, take a walk clear your head.
Then come back more focused