sqlite database table with 1000's of columns
Despite of the database you are using, normally you don't add thousands of fields to a table. Your second model is more 'normalized' ( and it's easy to index ), and should work better ( I'm not an expert, anyway ). My opinion is based on normal limits of databases, that are not meant to work that way, so you're going to hit some inner limit of the engine, or misusing the engine as it was designed for.

You can explore functions and datatypes of more modern versions of mysql, MariaDB and others, that have defined types for points and similar.