Are there any guidelines how the upkeep is calculated for owning a ship and a crew?
As house rule I decided the following:
- Depending on the type of ship the upkeep cost required to be paid at the end of its Sailing Range will be from 10% to 50%. Small vessels are in the lower category based on their crew and sailing range, largest vessels comfortably eat your party’s riches unless they fail to full the cargo with precious gems from their raids or deals.
- The upkeep covers food supply, crew salaries and maintenance activities done at sea and when docked.
- It covers re-supply of ammunition and repair of ship weapons if damaged.
- It does not cover damage caused by complications, hazards and ship battles.
- If the ship is operated by slaves the upkeep is reduced depending on the amount of slaves that the crew consist of (10-25% reduction)
Still have to test the numbers and see how impacts the game in the long run, but with the abstract item prices and economy (quite weird numbers in the Treasure and Gold chapter in the core book), this is for now. 
Let me know how you deal with sea adventures! 
Their house rules sound sound and real good, even I have some such thoughts. But after my players just survived the adventure, island of the black one (with crying in their throats). they have come across big riches that make them throw 10 gold here and 20 gold there. So then I do not have to think about their upkeep. But soon their luck is lost in the Deep sea 
Gold is never enough, especially when they start to have big appetite - fleet of sailing ships, mercenaries, small army, base of operation and open sea conflicts with pirates or some nations.
Yes it is so true