Hey! Great question - I believe when you create a new 'project' for your game on itch (before you submit it to the jam) you can make it available for more than 1 platform. For previous jams we've hosted we have had entries that are both run in the browser and run locally.
Given the desktop OS marketshare (Windows: ~85%, Mac: ~12%, Linux: ~2%), I'd say windows is probably the safest bet there - although that being said everyone will be able to play it if runs in the browser!
Hope this helps.