In this case, the present is absolutely correct. I would naturally say "I hope you're fine," or "I hope everything is good with you," if I hadn't heard from a friend in some time. "I hope you'll be fine" isn't a natural choice as it sounds like "I hope you will be fine in the future" -- and as you said, you're concerned about your friend right now. You can use "I hope you'll be fine" if your friend is about to try something risky -- but it sounds like you're worried rather than encouraging, so I don't use it much. "I'm sure you'll be fine" sounds much more encouraging!

You haven't heard from your friend for 2 weeks .The correct forms > I hope you are fine/I hope everything is fine (for/with you).By saying these, you hope that he is fine now ,wherever he is. You don't say , I hope you will be fine .which means you hope that he will be fine from now and beyond , and not regarding his current situation. You say it when you want to ASSURE someone that it whatever it is , it will be ok .eg .Don't worry , you will be fine ( staying with him) etc . And, I hope everything is good with you is correct , but I hope everything will be good with you is more a wish than a concern