A good question.
I suspect you'll get a different answer from each person who replies, though.
Counter storage is often determined by the individual's tolerance for compromise.
For example: my system counters are stored in two large, deep trays, each divided into 24 compartments.
Mine are older deep Plano 3700 boxes.
I could easily separate them into two more equal storage trays, given that most of the compartments contain at least two types of counters,
depending on several factors: their frequency of use, the quantity of each type, whether the counter type has a different function on the reverse side, etc.
I find two large trays plus at least one each for each nationality in play plus a separate smaller tray for acquisition counters used in a given game to be about all
I can manage on a normal sized dining table sized play area, along with charts, the rulebook, dicetower, and of course the maps.
I'm sure some won't compromise and will have each different counter type in it's own compartment, while some may even have more types combined than I do.
I find the 48 compartments to be a minimum for the overall quantity of system counters I have, which are more than are contained in BV.
Some of my compartments are quite full, yet I don't know if I'd really go as far as filling another large storage tray due to the added real estate needed on the table.
