Interesting plugin idea, and we'd be appreciative to see your final product! One suggestion I can think of to make your plugin more self-reliant is to associate the hashtags and other data outside of the paper's metadata page, and within the plugin's own interface, and store the data in a table specific to the plugin (see the static pages plugin
for an example of how to get a table unique to the plugin into the database), or even just in the paper_settings table. In the plugin's settings page, you could list each paper and allow the option to enter tags respective to that paper, which when saved will store the paper ID and tags in the plugin's table. This table can then be accessed (probably by another plugin) in the reading tools for each paper by looking up the paper ID and pretty printing the rest of the row.
I appreciate the complexity of that solution, but I'm not certain of an easier way without modifying templates and code. FYI, this type of enhancement has been marked as a feature suggestion
for the next major version of our software.
Let us know if you have any further questions and what your final solution is.