Bestemming usually means destination.
Depending on context, it can refer to:
In Die bestemming is by die see, the most natural meaning is the physical destination or place being referred to.
Here, by means something like:
So by die see means by the sea, at the seaside, or near the sea, depending on context.
It does not necessarily mean directly touching the water. It often simply suggests a location close to the sea.
Because Afrikaans normally uses the definite article die with see in this kind of expression.
So:
Leaving out die would usually sound wrong in standard Afrikaans here.
Yes, sometimes, but the meaning shifts slightly.
naby is more explicitly near.
by can sound a bit broader and often feels very natural for locations.
So both can work, but by die see is a very normal and idiomatic phrase.