First an answer to your question of the charass_target_type values:
PI: Purchase Order item
QI: Quote Item
R: this one has me scratching my head, unless its a typo, typically the R's are for Return Authorization (RA) or Return Authorization Item (RI)..
SI: Sales Order Item
W: Work Order
When you define a characteristic and associate it with Items (charass_target_type 'I'), it is implied that you can use that characteristic in the places that the item can be used, such as on a Sales Order Item, if you assigned "Brand" to an item you should be able to see that Brand on the sales order line item, so it makes sense to me that the PI/QI/SI/W types have entries, if you created those line items for an Item in your database, the characteristics would follow it throughout the application.
The reason I ask what version of xTuple is because as of version 4.9.0 we modified the characteristics structure a bit in order to make them extensible. Two things to point out, one being a table called "source", which is now the central location for information such as the charass_target_type values, if you look in the source table you will see the column "source_charass", which is where I pulled those target_types from. Additionally, there used to be columns on the char table to let the user indicate where that characteristic can be used (such as char_items, char_contacts, etc), however those columns have been deprecated in favor of a new cable called "charuse". This table is what keeps the selections of where your characteristics can be used. So if you choose to allow Brand to be used on Items, there should be an entry in charuse that maps your char_id to the charuse_target_type = 'I'.
We generally don't recommend clearing anything out unless its invalid data, but in this case I think you are just seeing artifacts of how the characteristic system flows throughout the application and the data is fine on its own. At minimum a row of data will take up the size of a block on the hard drisk, usually around 4KB for smaller rows like charass.. this won't have much impact on your database performance at all.
Lastly, I think you may have brought to light something that may be confusing, in that prior to 4.9.0 specifying an characteristic can be used on Items allowed it to be used in the places an Item can be used, however as of 4.9.0 the individual places have been broken out. Meaning, there are now checkboxes for Sales Order Item and Purchase Order Item, and checking that a characteristic can be used for an Item still implies those even though they haven't been explicitly selected. I will bring it up to our development staff and see how we want to handle that. Thank you for bringing it to our attention --
Hope this helps, let me know if you have any further questions.