Unless I’m missing something, there needs to be a better UI option for deleting items. If your inventory is tucked away in boxes and you hit max item limit, there doesn’t seem to be any reasonably way to selectively delete items.
The easiest way to do it is to sell unwanted items to a trader. If you have a market stall (or several), you can call up one trader per stall per day which means you should have no problem selling off all your surplus items quickly. Plus, the gold can be used to purchase high-tier storage items like vaults, which will allow you to further condense your storage for essential items and thus cut down on the number of crates, urns, etc. in use.
Another option is to build some basic input bins for raw resources you have a surplus of (e.g. wood) so that they’ll be filled as a priority, then you can delete the input bin along with its contents in one go.
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And, most stupididly simple of all: don’t produce what you do not need.
The less the ai has to handle, the better the game runs ( and the more effective your linhs at stuff you want them to do)
Amen to that! Although it’s the most common rookie mistake across the genre, and has been my single-most commonly repeated reply in a range of sim/management/townbuilding games.
I’m waiting for the day someone releases a game like this with a proper tutorial, one which walks the player through doing a large order and then doing the same order but broken into steps and not producing rampant excess of materials. It’s something which seems so obvious in hindsight, but most players get stuck in the tunnel of “more orders = more production” when the reality is that more organisation and less walking around gathering materials = more production.
why not just turn off the limit in the options and accept the possible performance loss
because that seems to be the problem the op has
Actually, it is not in a tutorial for a good reason. The fun of all these management games is to find that sweet spot where you manage to produce what you need with the fewest resources (meaning time, building, crafters). The end goal is to become as effective as possible to produce what you need. Same goes for Settlers and Anno for example but in their case it’s more obvious. Putting it in the tutorial would spoil the fun out of it. But it should be explained to some extent. Settlers and Anno does that well by taking a simple production chain as an example in the very beginning of the game.
Identifying where your hearthling are spending too much time to produce unnecessary resources and optimizing this may be your next goal in the game 
You can also embrace that trading gameplay style by doing a Rayya’s Children playthrough.