It's usual to read in common data files in the global section of the app, outside of ui and server (in a single file app the global section is the code before the ui definition, or it could be in a separate global.R file). Then it only occurs once and will be available to all users of the app.
I'm not sure how shiny handles files in subdirectories, have you tried putting the file directly in the main project directory?
Your file is still quite big, you might be able to reduce the size further by recoding, filtering, etc.
https://shiny.rstudio.com/articles/scoping.html