Node theming through Views or tpl.php files - which one is better for performance? As an example, let's take a node with 5 fields and two blocks between those fields. E. g. you want an article do be displayed like this:

First field

Second field

Block with related nodes

Third field

Fourth field

Block with ads

Fifth field

In D7, such display is quite simple to create with Views - you use contextual filters to output fields and just put two blocks between them.

Another option is to use node.tpl.php and create the same template.

Which of these two (Views with context. filters and tpl.php files) is better performance-wise, especially when it comes to MySql performance?
The two are essentially doing the same work and are going to degrade over load very similarly from my experience. If you look at how views works and builds its content, contextual filters is just aiding the discovery by passing in all the data the view needs. This has to be done one way or another. After that, the view builds the same regardless. 

However, tpl files are greatly useful for code management. If you are really worried about performance, then you need to look into memcached and/or Varnish - both are open source and can be implemented easily on most *nix servers.