Hi, the 'place' based Story Map apps that display images side-by-side with and linked to a map aren't really designed to handle a very large number of images. The average Story Map Tour has probably 30 places (and maxes out at 99 unless you customize the app, the average Story Map Shortlist probably 80 or so divided divided into tabs, and Story Map Crowdsource a few hundred. You wouldn't want to try and put thousands of images in these place-based apps both for performance reasons and also because their user interface is browse- rather than search-based. Here's a Story Map Crowdsource that was prepopulated with more than 1000 historic Japanese postcard images: https://ej.maps.arcgis.com/apps/StoryMapCrowdsource/index.html?appid=3625639d89454282b44c7eb899fc910... .
If you have a web map with a layer containing several thousand points, each of which can be clicked to display a popup that includes an image, you could include that web map in one of our 'narrative' based apps, like Story Map Journal, Map Series, or Cascade. If you use another one of the configurable apps in ArcGIS to publish that web map, you could also embed that app into a narrative-based Story Map app to combine it with text and other multimedia. In both of those cases, the Story Map app is simply displaying a web map or other app, so the performance should pretty much be the same as viewing that map or app outside of the Story Map.
Hope that helps. Perhaps tell us more about what your specific application is.
Rupert
