Hey Antonio,
You've got a lot of questions here, so I'll copy and paste a bit. We started in a similar manner as you, but my first partners were bankers and title people, so we had a background already in this. We still are partnering with others to do deals. So I'll answer your questions with how we do it...
Should we do an LLC for the joint Venture? An LLC or S-Corp is like an entity with several owners. You will come to an agreement on what percentage of the entity you each will own, what percentage of profits you'll get, who'll provide what capital, who does what, who can sign, etc. You'll create an "Operating Agreement" (LLC) or "Bylaws" (S-Corp) to spell that out. An LLC would be a good vehicle for multiple owners. Good fences build good neighbors, so make sure everything is agreed to in writing in the Operating Agreement or Bylaws.
Under whose name does the property go under if buying with an LLC? The entity owns the property. It has similar rights to a natural person including that of property ownership. You and your friends own the LLC or whatever entity you go with.
Should we get a mortgage on our names in order to avoid having to take a commercial loan (Min 25% down), and how does the mortgage work with a Joint Venture ? Unless one of you is going to own the property personally or if you all go on the loan, this wouldn't really work well. Conventional loans for investment, non-owner-occupied property are likely going to require 20% down anyway. Low down payments are usually for owner-occupied property.
Can you refinance if you have an LLC for the property, or is it better to move the property to an LLC after refinancing to avoid the due on sale clause? Technically, the due on sale clause is triggered when property title transfers, so transferring it after you refi would technically trigger it. That being said, that would be highly unlikely. If you get a commercial-style loan, simple have the closing agent/title company make the change as part of the closing. Disclose what you're doing with the lender and have them shepherd you through that process. We do it all the time for borrower and we buy our investment properties in LLCs. This won't be difficult.
Would the deed have the LLC or the LLC holders? In most jurisdictions, the deed is recorded and that is part of the official record. If Snidely Whiplash (for Dudley Dooright fans) steals the deed to the property and ties Nell to the railroad tracks, the recorded deed is still in the name of the LLC. Someone can stick the paper deed in a safe deposit box, but it's no longer as important as it once was.
If you have any more questions, let me know. I'm happy to help. I do hope that helps you.