At the moment, the series information on the Kobo devices is only used in the library lists and during a search. It shouldn't have an affect on the performance anywhere in the device.
But, I think you are actually using the series column as the shelf column. Which means you are creating a shelf for each series. In that case you will have 2000 shelves with your 5000 books spread over them (assuming they are all in a series). In that case, opening the shelf list will take a long time. But, I know someone has reported similar figures before and was able to get to the shelf list. They decided it didn't work for them as there is no way to search for the shelves and the list was just to long.
The restart and insert time can be beaten by not powering off the device. Just let it go to sleep without powering off. This uses virtually no power and the battery will last a long time in this state.
After the turning the device on and inserting the SD card, is the black processing screen displayed? Or is the half hour how long it takes before the device shows the books on the SD card in the library lists?
As to the query in calibre, I don't think it can be done. The search and templates work on metadata for a book and can't refer to another book. You can easily select all books with a particular value in a column. You can also select all books in a series. But, I don't think you can combine them in the way you want to.