You're begging the question here. When presented with an argument that Cuba's natural trading partner is the US but that they are prevented from significantly engaging in trade by the embargo and that this impedes their economic development you say yes, but their largest current trading partner is in Europe so it's not such a big problem.
Well, let's get a little more precise. I was presented a CLAIM that the US was Cuba's natural trading partner, not an argument. My point about the Netherlands is that proximity alone does not indicate natural trade partnership, because such an arrangement should favor nearer European countries over farther ones, and that's not the case. A natural trade partnership would depend on Cuba offering the US good that the US wanted to buy at attractive prices. Cuba does not, for example, export much sugar to other sugar producing countries nearby. An ARGUMENT that the US is Cuba's natural trading partner would present what goods Cuba has to offer at what price, and what price we pay for those goods from other sources.
Furthermore, embargoes are not the only source of trade barriers. For example, sugar subsidies and quotas are common, and present barriers for MANY countries. How do the effects of such trade barriers compare to the embargo? Would Cuba still be able to export much sugar to the US if, instead of an embargo, they just had to confront the sort of sugar tarriffs/subsidy schemes/quotas that we (and so many other countries) have in place? Would Cuba gain more from lifting of the US embargo, or from lifting of Europe's CAP subsidies? I'm actually not sure, but I'm far from convinced that the embargo is the primary trade barrier for goods.
If we were to drop the embargo and Castro were to soften his stance towards the US a bit, the US would soon dominate trade with Cuba again. Prior to the embargo, nearly 70% of Cuba's trade was with the US.
Proximity used to matter more than it does. Agricultural subsidies also distort markets more than they do. Trade balances shift over the course of decades, and there's no reason that we should expect it to come back to balance. Plus, the statistic is misleading to begin with. Suppose I can buy a can of coke at one grocery store for $1, and at a second store for $1.01. Suppose I buy 90% of my coke from the first store, and 10% of my coke from the second store. If, however, I'm prevented from entering the first store, I'll go to the second store for 100% of my coke purchases. The amount of coke I purchase will be only slightly diminished by the extra cost, it will NOT be diminished by 90%. We can expect that the trade Cuba would do with the US if able is not disappearing, but mostly shifting to slightly (but likely not significantly) higher cost producers/lower cost buyers elsewhere. The economy is globalized sufficiently that the implied impact in your 70% figure simply isn't going to materialize anything like that large in the actual impact.
Apart from trade, we're overlooking one of the most important things the US has to offer Cuba, and that's tourism. It's a vital sector of Cuba's economy these days (as it once was), and is almost single-handedly responsible for pulling Cuba out of the Special Period.
Tourism is the only significant trade source which can't simply redistribute, and you might have a point there.