If deployment time is exceeded, all that happens is lowered morale of the crew. The morale however, does not affect commercial ships in any way that I know of. As such I always have most commercial ships, like freighters or fuel harvesters, on three months of deployment time, despite the fact that they almost never go back to the colonies.
For military ships it's a different matter, as it affects a lot of things such as targeting. Deployment time does not rise if a ship is above a colony with some people on it (10k is the minimum I think). As far as I know geological and gravitational survey sensors are affected by morale, so if a survey craft has exceeded it's deployment time, it will survey slower.
If you exceeded your deployment time, all you have to do is to send your ship to a planet with a population and wait.