According to this document http://www.basket.ee/uploads/docs/XXsaj.pdf Basketball first came to Estonia in the 1910s as near-by St. Petersburg's team wanted to play with someone. By 1920, it was played in a couple of schools. As Estonia has weather which doesn't support outdoor sports (too cold, too rainy or too little snow) that much anyway, then basketball was a good option (cheap, very little gear needed). Some foreign instructors came to Estonia and enthusiasts went abroad to study (Estonia was independent at the time). For a small country, any kind of international sports competition is lucrative, so I guess that plays a part as well. Being an enthusiast in the first twenty years could secure you a place in the national team quite easily. As for Lithuania - one of the tallest nationalities in the world, so maybe that helped as well?

It's also super popular in Spain. I have no idea why.

Does anybody know?

The Gasol brothers, for example, were born and raised in Barcelona, and they both play in the NBA.

Spain vs. USA at the Olympic finals is already a classic at every Summer Olympics.