This answer is correct to the best of my knowledge however, I am not an expert on the subject. Also, I am referring to the "old version" when mentioning TCPDF, not the new version that is under development.
Why this occurs
Helvetica is one of the standard 14 or core fonts that should be compatible with most PDF readers. This means that the fonts can usually be used in a PDF without having to embed it in the PDF document. You can see a list of the core fonts in the TCPDF documentation. The "helvetica.php" file in the TCPDF fonts directory is not a copy of the Helvetica font. The file is only a description of the font as described here.
The downside of using these core fonts is that you are relying on the version of the font included with each user's PDF reader or installed on their systems. According to this Wikipedia article, some PDF readers will substitute similar fonts and these will often have different character sets. I assume this is done to save money on licensing fees for fonts that are not open source.
In your situation, I am guessing that your PDF reader is not using the same font that is installed elsewhere on your computer. It is likely using a substitute font that is not the Helvetica® font designed by the Linotype Design Studio.
Solution
I have encountered a similar situation in the past and solved it by embedding a free open source font in the document. This included creating custom characters that would never be installed on a user's computer. PDF readers will use the font embedded in the document to render the PDF. The embedding process requires that you first convert the font’s TTF file using the TCPDF addTTFfont() method before generating the document with TCPDF.
Converting and embedding fonts is discussed in the TCPDF documentation and in this related answer about font conversion: https://stackoverflow.com/a/19394545/9356981
Licensing fonts
Licensing and embedding the Helvetica font is one option, but this could get very expensive. You may want to search for open source fonts on services such as https://fonts.google.com which includes a Greek character search filter.