Late to the party and what a neat project!
Don't know if this would help but these showed up on a search...
https://www.ebay.com/itm/400979383636
I am guessing at "pea size", it taxes my pea brain. These would have a pre-drilled hole that one of the micro LEDs might fit in, maybe secured with some UV cure acrylic cement. Perhaps the frosted finish might diffuse light effectively. I suspect other sizes are available as well. They showed up using "round clear acrylic beads" as a search term.A global search you might say (or not).
Sorry for the spam if this is not useful and give my regards to Captain Nemo and crew.