I am an old-school MySQL user and have always preferred JOIN
over sub-query. But nowadays everyone uses sub-query, and I hate it; I don't know why.
I lack the theoretical knowledge to judge for myself if there is any difference. Is a sub-query as good as a JOIN
and therefore is there nothing to worry about?
Sub-queries are the logically correct way to solve problems of the form, "Get facts from A, conditional on facts from B". In such instances, it makes more logical sense to stick B in a sub-query than to do a join. It is also safer, in a practical sense, since you don't have to be cautious about getting duplicated facts from A due to multiple matches against B.
Practically speaking, however, the answer usually comes down to performance. Some optimisers suck lemons when given a join vs a sub-query, and some suck lemons the other way, and this is optimiser-specific, DBMS-version-specific and query-specific.
Historically, explicit joins usually win, hence the established wisdom that joins are better, but optimisers are getting better all the time, and so I prefer to write queries first in a logically coherent way, and then restructure if performance constraints warrant this.