As a player, I hate getting a bunch of items that I must carry, that do not do anything but hold some scripters check box.
As a scripter I understand the need to check a item to see if something happens.
I tend to use the PC skin to hold all info, and the campaign database to hold all conversational type info.
As far as your question, it has been my experience as a DM, most players have no sense of organization when it comes to their PC inventories. If you give them bags, for specific things, they will cram them full of something else. If you say keep these things on your first page of your inventory, they will place them on the second to last page, because they have no idea what a first page is. Most players believe that any help out rule, but not enforced rule, does not apply to them. Simply a fact of gaming I guess.
What lags out in terms of inventory seems to come when there is more than 3 containers in the inventory, when the inventory is nearly full of little junk, and really only shows up, when the PC logs in and out of the server. Using the smaller containers, say the misc small, and misc thin items from CEP tend to push it down to 2. the more items, the more lag. In crafting mods, it can be a nightmare. Stacking does seem to help, but if the inventory is full of stacks, it can be even worse.
good luck!