Hi Leila,
Yes, the Fees plugin (the one named "HikaShop - Fees", not the Global cart fee one) can do exactly this. It adds a fee to the cart from a formula you write, with a condition so it only applies when you want. You will not have to do any maths yourself, the two lines below are all you need.
Add one formula with:
Condition (so it only applies to EU orders):
{cart.cart_shipping_ids}==XReplace X with the id of your EU shipping method (System > Shipping methods, the id is shown in the listing). Since your EU shipping is already restricted to your EU zones, this is what limits the fee to EU-bound orders. If you have more than one EU shipping method, add one formula per method.
Formula (3 per product type, quantity ignored):
{item.cart_product_quantity}*0+3
How it works: as soon as a formula contains an item or product tag, HikaShop evaluates it once for each product line in the cart and adds the results together. The "*0" cancels the quantity, so every distinct product adds a flat 3 whatever the number of units. So 3 spoons (one line) + 1 plate (one line) = 3 + 3 = 6, which is what you need. The quantity is never multiplied in.
Give the formula a Label (for example "EU customs fee"); it will show as its own line at the checkout.
One thing to check: the amount is added in the cart's currency, so a customer paying in euros gets a 3 EUR fee and a customer paying in pounds gets a 3 GBP fee. Make sure the currency shown at checkout for your EU customers is the one you intend.