(I was pulling my hair, failing to google any useful info about the shipping to Czechia. So I though I'd share what I found out, sorry for necro posting.)TL;DR: there was no additional cost on delivery, with no bureaucracy needed on my part, whatsoever. I shipped $4 worth of boards from JLC with the cheapest "Global Standard Direct Line" to Czech Republic.
As @wraper posted, JLCPCB lists the "Standard Direct Line" shipping option in the "IOSS" section. This is the mode where you pay VAT (21% for CZ) during checkout and the company (JLCPCB) then pays the collected VAT back to the destination country. (in bulk, on monthly basis)
Import tax to EU isn't supposed to be paid for goods under €150 (this limit does NOT include the shipping cost), but you need to pay the VAT for
all goods (VAT always DOES include the shipping cost). In the IOSS mode, this works well between the companies and the state.
But! Then you have to prove to the Customs that VAT has already been paid, and sometimes a fee for this process. Somebody needs to pair the package with the VAT payment (

) and the carriers might charge you for this. The Czech Post currently charges 0 CZK for Customs clearance, if you are using the IOSS mode, but often you don't know in advance who the last-mile carrier will be, Czech Post or a private company. Their methods differ. Luckily, anyone knowing {tracking number, IOSS number, goods description} can fill in the data.
- For example, for ebay stuff, the IOSS number is publicly known, and you are supposed to submit a Customs declaration to the Czech Post (I tried this successfully for SpeedPak and "Free" shipping options) or on the eCep portal (haven't tried yet) manually yourself, to prove the VAT has been paid, to avoid paying the VAT yet again.
You get the tracking number (once/if they give you one that has a compatible format), the IOSS code and fill in addresses, value and HS codes (type of goods) yourself. If this works, they charge you 0 CZK for paperwork, and do not charge any additional VAT. This has worked for me 3x already. - For JLCPCB, the IOSS number is not provided (I tried asking) to individual customers. I think they fill in the customs declaration data for you! This is probably why I didn't need to do anything at all, just wait.
My package first arrived to Hungary (this matters, because the Customs check is done in the first EU country on arrival), then was forwarded to Czechia and the last-mile carrier (Czech Post).