This was asked by someone else, and answered by Joan on the XD team, so I've read the answer!
When there were arrows people would often use them instead of using the hot spots that you have set up as your way to navigate, which defeats the purpose of the test. So now there are no arrows if you have linked hotspots for navigation. There are arrows if you don't have links, and there are also arrows for the note taking feature.
Wow, that's not too impressive. The best solution would obviously be to have both options as XD creates visual flash effects on the spots in the layout that's linked anyways. To be able to just flick trough the layout by clicking conventional links was a very nice way to do just that, namely flick trough the layout without assessing the navigational aspect of it. If this creates such a confusion then why couldn't they just hide the pagination with a text saying "Show/hide text link" or something? Why can't Adobe put themselves in the normal user shoes for once? It's amazing.
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I was a teaching assistant in two of Paul Trani's XD sessions at MAX, and he was thrown a bit by the arrows not working. Having already seen the questions here I knew what was going on, and was able to tell him to show the comments feature in order to page through the slides. I had a discussion with the XD engineers afterwards, and suggested that maybe there should be an author time option where you could set it to allow the user to arrow through the slides instead of just using the hot spots. There is a Provide Feedback option that you could use to vote for that idea, or propose it yourself if no-one else has.
In a near future update you'll be able to turn of the highlighting of hot spots feature (if that didn't get into 1.0). Some people find that distracting, or at least ugly. It's not ideal for when you're doing a demo and need to remind yourself about where you put hot spots, but it can be better for user testing, where the user has to reason what to do next, instead of mousing around until something lights up.