Yes, the converter only converts .mq4 to .mq5 files.
MQL4 is a programming language and .mq4 files are the files containing the MQL4 source code, which is a human-readable text.
.ex4 files contain binary data, which is not human-readable. These files can only be read/executed by MetaTrader. Open such file in Notepad and you will see. I guess the "ex" in the extension name means "executable", although these files are not self-executed like .exe files.
If there is a tool to convert the data in .ex4 files to human-readable MQL4 code, this tool would be called Decompiler. But I'm not making such tools.