Which of the join and subquery queries would be faster and why? When I should prefer one over the other?

Well, I believe it’s an “Old but Gold” question. The answer is: “It depends!”.
The performances are such a delicate subject that it would be too much silly to say: “Never use subqueries, always join”.
In the following links, you’ll find some basic best practices that I have found to be very helpful:

• Optimizing Subqueries
• Optimizing Subqueries with Semijoin Transformations
• Rewriting Subqueries as Joins

I have a table with 50000 elements, the result i was looking for was 739 elements.

My query at first was this:

SELECT  p.id,
    p.fixedId,
    p.azienda_id,
    p.categoria_id,
    p.linea,
    p.tipo,
    p.nome
FROM prodotto p
WHERE p.azienda_id = 2699 AND p.anno = (
    SELECT MAX(p2.anno) 
    FROM prodotto p2 
    WHERE p2.fixedId = p.fixedId 
)

and it took 7.9s to execute.

My query at last is this:

SELECT  p.id,
    p.fixedId,
    p.azienda_id,
    p.categoria_id,
    p.linea,
    p.tipo,
    p.nome
FROM prodotto p
WHERE p.azienda_id = 2699 AND (p.fixedId, p.anno) IN
(
    SELECT p2.fixedId, MAX(p2.anno)
    FROM prodotto p2
    WHERE p.azienda_id = p2.azienda_id
    GROUP BY p2.fixedId
)

and it took 0.0256s

Good SQL, good.