Currently we have tables and indexes in separate tablespaces. We're planning on converting the tablespace with the tables to large. Is it best practice, to also convert the tablespaces with the indexes to large also?

I'm not sure what the best practice is but I would. Especially if the index tablespace is close to the max limit. Your data tablespace will be able to grow using the new limit so your index tablespace may need more space at some point too.