I would personally probably say in most contexts:
to mean "In Japan, what kinds of sports are popular?".
Your first sentence is slightly incorrect, as you shouldn't use は when the topic is undefined (you don't know which sports are popular), and so making minimal edits should read:
Your second sentence is grammatically fine, but means something different: "In Japan, are sports popular?" -- you might just get a yes/no answer to that question, whereas the first suggestion above should elicit a more detailed response.
The same structure can be used for other similar questions too. For example:
would mean "What sorts of cosmetics are popular in China?". Just change the noun and location of interest!
You might have to change the question word you use when it comes to more specific questions. Your question "Which bars are popular in Tokyo" would probably not be well understood if using どんなバー, as that would elicit responses about the types of bar that are popular (e.g. a hostess bar vs a hotel bar vs a sports bar). If you are looking for specific information about which bar, rather than what kind of bar, is popular, you would be better off using どのバー or どちらのバー.