Actually, Brussels and Gent were already more important than Amsterdam and the Hague prior to the Eighty Years' War in OTL. During the 15th and 16th century, Flanders was economically one of the most important regions of the Netherlands, and during the time of Charles V/Karel van Luxemburg, the Flemish city Antwerp was by far the largest and richest city in the Low Countries.
Agreed, the south was by far the most important part of the Low Countries.
As a matter of fact, even in 1830, when Belgium seceded from the United Kingdom of the Netherlands, it had a population of 4.5 million versus the North's 2,5 million. (Nowadays it's 16 in the Netherlands and 10 in Belgium: how things have changed...).
Another interesting factoid: during the Second Anglo-Dutch War (1665-1667 or something), the total urban population of the Republic in absolute numbers was larger than the urban population of England and the Spanish Netherland's urban population was at least half again as large at the time.
The advantage this gave the Republic is clear when realised that the cities provided the largest part of taxes by far. During the war, the Republic was able to outbuild the English seven to one in ships, for example. Other factors also played a role, like having a larger merchant marine than the rest of the world
combined, but this large constant source of revenue also played an important part.
In fact - it is only because of the Spanish conquest of Antwerp went into a sharp decline. Just over half the city's population fled after the fall of the city, and almost all of the refugees from Antwerp fled to the northern Netherlands, and many of them ended up in Amsterdam.
In fact, it is even quite likely that, if Antwerp hadn't fallen to the Spanish,
Amsterdam would never have become the economic centre of the Netherlands.
The economical centre probably not, although it might depend on where the VOC or its analogue starts the world's first stock exchange. If it's Amsterdam as in reality, it might very well still become the financial centre of the Low Countries. Amsterdam was already rapidly growing in th period leading up to the Eighty Year's War and was advantageously positioned to take advantage of the Baltic trade which generated the majority of the Republic's trade income during its Golden Age. It would still have become the economical centre of the North in the 17th century.
Of coure, in this scenario, Antwerp won't ondergo its disastrous sack and the closing of the Scheld and would probably remain a bigger city than Amsterdam and a major (quite likely still the largest of the Low Countries) economical centre in itself. And with the amount of money available around 1600, the VOC would probably place its main office in Antwerp instead of Amsterdam.
It is also noteworthy that, IIRC, Antwerp was the capital of the Dutch separatists until its conquest by the Spanish in 1585.
True, although William the Silent was based in Delft from 1572 to his death in 1584.
If the Eighty Years' War would end in a total defeat for the Spanish,
it is actually quite likely that Antwerp becomes the capital and economic centre of the Netherlands.
Depends, it could also revert to Brussels, which was the capital since the Burgundian era (after first Bruges) like before the revolt. Antwerp is definately the most plausible second choice though, way before The Hague, which was a sort of compromise after Antwerp was captured by the Spanish in 1585.
As an aside, it would have probably gone to Delft if it had been decided The Hague (which had just been sacked by the Spanish) was not worth the effort rebuilding.