The first one is closer to being correct than the second one. Here is the correct version, assuming I'm interpreting the meaning correctly:
Even if this approach scales for a large number of similar nodes, it is impractical for a heterogeneous system.
There were a couple errors in your first sentence:
- The first use of the word scale should be plural, since the object which is performing the action is singular. If the sentence read "these approaches[...]" rather than "this approach [...]", scale would have been correct.
- You missed the letter a before "heterogenous system". You probably just accidentally left it out, but just in case you didn't, the word a is placed before a singular noun, usually when referring to a general, arbitrary example of something.
Now, on to your actual question -- "Even if" shouldn't be separated from the rest of the clause with a comma. A comma typically implies the end of a clause. "Even if", in this case, is a qualifier for the rest of the clause ("this approach scales well for a large number of similar nodes"), which means that it gives additional meaning to the clause. Because of that, it should not be separated.
This was a bit of a tricky question to answer. It's really just one of those phrases that you have to just hear a few times and let it become natural.