I was trying to continue playing my older save, and was surprised that items don't show any info in Factoriopedia.
In the source code I saw that this was a deliberate decision and not a bug. I must admit that I used FNEI in 1.1 and was looking forward to the Factoriopedia integration. Factoriopedia also doesn't reveal the secret stuff (unlike FNEI), therefore I would suggest to add it as an user setting.
Great mod, I really enjoy the unique challenge!