The ships that discovered and plundered the new world were made almost entirely out of biodegradable materials and lived very rough lives, sailing between cool to tropical climates, through storms and damaging conditions, were vulnerable to rot and fire, and in later centuries, could be subjected to extreme violence. It seems many (most?) were decommissioned after being deemed broken beyond repair, or condemned by underwriters on economic grounds, as opposed to being retired due to natural degradation.
In a hypothetical scenario, how long would a ship like the Santa Maria, Sao Gabriel or Victoria, if maintained well, be expected to remain in active service back in the day?
I'm not sure I'm following the question -- all the ships you cited led somewhat short lives because they were used on voyages of discovery far away from basic maintenance facilities (ports, etc.). It's a bit like asking how long a car will last if you never change the oil or filters or replace the tires.
Are you asking how long a ship would last if regularly maintained and not subject to fire/storms/loss in battle? If so, the answer is basically forever if budgets are unlimited -- look at HMS Victory or USS Constitution.
A reasonable lifespan for a wooden ship that's not a national treasure could be easily 50-100 years. Even Victoria, once repaired after returning in 1522, was in service until 1570.