whether to merge partitioned table with only partially overlapping columns
Having all your data in fewer, common tables is obviously going to make your coding simpler.  I would suggest you pursue this option.

Partitioning is not that scary.  Annualised data like yours is the archetypal usage for partitioning.  It will help with your query performance and may help with your data management tasks (load / delete), depending on MonetDB's capabilities.

You say some data is in different formats in different years - tinyint v/s character.  This will be a problem for you whatever architecture you choose because you will eventually want to combine these in one resultset.  Fix this sooner rather than later.  Fixing in the data and table definition will be less work overall than fixing it in each query as you write it.

In summary 1) Fairly, especially if you have to reconcile type differences 2) "A bit" if your queries are simple to "a lot" of you get it badly wrong 3) not a MonetDB expert but most RDBMS handle data many times the size of RAM without problem.