No, Pythonista 3 is a separate app, so you need to purchase it again. For a while after Pythonista 3 was released, there was a bundle with Pythonista 2 and 3 in it, which allowed you to get Pythonista 3 at a lower price if you already owned Pythonista 2. This is no longer possible though. (Pythonista 2 is also no longer available for purchase - Pythonista 3 supports both Python 2 and 3, so there's no advantage to buying version 2 instead of 3. If you already own the app, you can still redownload it of course.)

If you do buy Pythonista 3, there is one upgrade-related feature that you can still use. If you go into Pythonista 3's settings, you can enable the "Pythonista 2 Files" option. This shows your Pythonista 2 Script Library as a special folder inside the Pythonista 3 file list, which you can use to easily transfer your files from Pythonista 2 to 3, using the normal "move" button in the file list. You can disable the option later to hide the Pythonista 2 files again (nothing will be deleted of course).