These rule have been Law since 1880, do you think that it was not practiced before then? Columbus's voyage was not a Military Expedition, so readers who expect to see the ringing of the bells in the log are wrong.
The original use for a ships bell had nothing to do with warnings per navigation rules. One of the most common uses was for the telling of time on the ship. When the hourglass ran out, the bell was chimed to signal it had been turned.
Now, here we go. Timing was a relative new thing in the late 1400's, because time was used for distance calculations, and to really use this, you need to have a map.
There are records of ships bells all the way back to the Bronze Age.
Another use, somewhat lost, was the use as a ranging device. In inclement weather, especially fog, they would sound the bell would listen for the echo. No echo meant nothing out there.
If there was an echo, it meant there was some sort of obstacle out there. Counting the time to the echo game them a warning of the distance to the obstacle, closing on it or moving away from it.
Think of the ships bell as the old school predecessor to Sound Navigation and Ranging. (SONAR)
I can certainly see why a recovered bell would not be from the Santa maria, and there was ample time to recover that wreck and use the timbers, so nothing would have been left such as the bell, as a shipwreck artefact.
But the bell comments take me back. While there may not be the mention of the use of the ships bell for timekeeping, there are other recorded uses. Bells have been used for a long, long time for various reasons.
I recall reading that on the Columbus trip, the natives were amazed by the sound of the ships bell? Not to mention adding bells to themselves and the animals to scare the natives.
Why would the Columbus fleet not have bells?