This may be oversimplistic for many people's use cases, but personally I write my notes in Markdown and store them all as plain text in a Dropbox folder. I search them the same way I search code with The Silver Searcher (`ag`) [1].
It works well for me and I don't run into any problems with being locked into software that's either not interoperable with anything else, or which is no longer maintained a few years from now.