First, don't rely for this, which is essentially a legal question, on tutorial like from Sparkfun. US rules
do not apply in Europe! In fact, the system is completely different in EU.
Assuming you handle your business stuff (tax, prices, business license, etc.) which are controlled by your government, then there are rules you need to obey when bringing a product to the market. That's mainly the CE marking and the WEEE directive (electronic waste). These are EU-wide but you need to consult your local laws to understand how exactly they were transposed into Croatian law - it differs, e.g. the German implementation is infamous for its bureaucracy and rigidity.
It says its ok to sell sub assemblies. So would then that allow sales of development boards, shield boards, etc... ?
That's US, doesn't apply in EU. That said, CE marking is self-certified, so you need to supply the declaration of conformity for each product - basically saying that gizmo XYZ complies with all the relevant norms - and then you can put the CE mark on your product and sell it. However, you are legally responsible for it, if there is any trouble or the authorities decide to spot check (e.g. the German ones do), you need to have documentation to justify your steps. One way to get it is to do the EMC (and any other required) testing at an accredited lab. Or you can even do it yourself, assuming you have the relevant skills and equipment.
AFAIK, items that are meant to be integrated into other products (modules, etc.) don't have to be certified but then they are not meant to be sold to end users. This is a grey area, IMO. That was why either Sparkfun or Adafruit started to certify their products, even though strictly speaking they may not have to.
Also, since its the IoT age, can such boards contain RF stuff like bluetooth, wifi, NFC/RFID, and use 433MHz transceivers?
AFAIK, not relevant, you still have to obey the same rules. Just when the board has RF, there are more and stricter rules to follow.
Can I then just say that the boards are not certified, and only allowed for hobby or development use?
No. You can only sell them as components meant to be integrated into something else, not as final product. The "hobby or development use" plays no role here. As components they may be excepted from some of the paperwork, but check your local laws before you do it. It is not very clearly defined and if the regulator comes to a different conclusion than you as to whether your gadget is a completed product or a component, you will have problems.
Also, is there a difference if the sold boards are open source, or if the schematics and documents are only allowed for buyers?
From a regulatory point of view there is zero difference, AFAIK. The neighbors TV receiving a ton of interference really doesn't care whether the noisy gadget causing it is open source or not. If you have sold it, you will likely get in hot water with the authorities either way. This is only your business decision.