The maintenance clock shows you how long a ship has not been properly maintained.
The clock starts at 0, and then increases over time.
The higher it is, the more often your ships suffer from maintenance failures which will have to be fixed using maintenance supplies.
This happens automatically.
There is an exception to this system, and that is Commercial shipping.
A ship that is classed as commercial, and thus built in a commercial yard, isn't build after military standards..yadayada.. doesn't fail.
Your Colony ship is very likely such a commercial design, and is thus fine with a single engineering space and will never break.
Unless shot.
Your military ships have a chance of a maintenance failure every 5 second increment, and their clock will slowly increase, thus increasing the chance for failures.
You can prevent this by keeping them at a Population with maintenance modules sufficient of maintaining the appropriate ship size or more.
Otherwise, regular overhauls, best every two years depending on your ships maintenance capacity, are recommended.
Maintenance supplies don't come from thin air, after all.
