Are there any restrictions on using Enterprise Manager Cloud Control in ECL 2.0 environment?
No. There is no particular restriction as ECL 2.0 when using Oracle Enterprise Manager Cloud Control (hereinafter referred to as EMCC).
However, as EMCC requires Oracle Database Enterprise Edition (EE) as a repository DB, Oracle Database Standard Edition 2 (SE 2) can not be used as a repository.
So you need to install EE separately, or prepare a separate server and install EE in it.
As for the above EE license, in case of using EMCC repository, purchase of license is exempted only when DB is single instance.
However, if you configure RAC or Data Guard, you will need to purchase additional licenses.