Was reading about the shipwreck of the "San Pedro de Alcântara" and it's said the ship suffered with not being water tight enough, needed a constant use of pumps. So what was the standart for ships around 15-17th century?
Not particularly waterproof! But then again it's a commonplace that all ships leak, even modern ships. Here's a beautiful picture of the USS Idaho from the 1930s, and you can clearly see that even at anchor in calm waters, the ship is pumping water overboard. This is an even clearer picture of USS Florida doing the same, from around the same era.
Wooden ships would leak even more than metal ships, because of the nature of their hulls -- even when fastened well, they would flex in a normal sea, even more so in a storm, and all ships were equipped with pumps to bail themselves out. Spending time in tropical waters, which the San Pedro de Alcântara did, would often also result in major infestations of the teredo shipworm, which is still a problem in wooden construction today -- the shipworm would literally eat wood, boring holes in a ship's hull. The Royal Navy used lead and eventually copper sheathing to combat the shipworm.
If it helps, I've written about ship construction and "classes" of ships in the age of sail before:
and about coppering here:
https://www.reddit.com/r/AskHistorians/comments/2709jm/how_would_a_britishhms_frigate_built_in_1715/
The fact that the San Pedro was built of mahogany may have mitigated somewhat against the shipworm -- mahogany is like a lot of tropical hardwoods in being, well, extremely hard.
