Looking at the points you raised around the difficult of the type of research and addressing each one of them:
Multiple feedbacks: multiple personas can use the same product
I think this is fundamentally not that much different to multiple personas that can use the same product in a B2C setting, but you might have to group each persona under a specific business to get a more clear picture about how different (or similar) personas exist in different types of businesses.
Low incentive to share internal problems
There are always direct and indirect ways to gauge the type of problems that they may have. I think the common way is through professional services and support that you can offer to them as a starting point if you are not able to engage with the end-users directly. But these organisations may also have their own internal UX teams that you can build relationships with. If they can see value of providing information about their problems then it is more likely that they will.
Long feedback cycle
I think this one is dependent on the way that the business operates and how quickly they adapt to changes. But it is a very real factor that you just have to take into consideration. Maybe this might also dictate or influence your own product release cycles and how proactive you are with addressing issues.
Small market (#): some markets are made up of less than 50 companies
I don't see the market size as having that much of an impact on the product discovery process. You would probably get the trade-off of having a more targeted research because of the smaller number of companies you have to go through.
Strongly based on relationship
This could be challenging if you don't have good business development and contacts within the industry or if you are relatively new and don't have a standing reputation. However, I don't think this has impact on how you would conduct the product discovery process differently to a B2C setting.
Domain complexity: some B2B niches are very specific and technical
I wouldn't treat technical businesses that much different to technical users. In fact it is more likely that the business will have a similar mindset or perspective as the end-user.
