I want to achieve an effect, of a country map (Greece in black background) with thin parallel white lines running through the map (for visualization, you can think it will be similar to IBM Logo -but with much thiner lines).

No matter the compound path I apply, the map is always broken in many different objects and can't make a unified object so I apply clipping mask to achieve the effect I want. I ve also tried to use a negative square where I would imprint the lines but in no avail.

Is there any limitation with complex objects I m not aware with? Is there any other way I can achieve this effect?

I m running 21.1 64bit version

Imho, there's a much easier and flexible way to achieve what you want.

You can create a very simple pattern based on a single line.

Set the wanted thickness and gap with the pattern options panel.

See https://helpx.adobe.com/illustrator/using/patterns.html for more details about how to create and apply patterns.

Select your map and, in the Appearance panel, create a new fill. Apply black color and the pattern you created to each of them.

Now, if you need to modify your pattern (i.e. make line thicker or change color), just double-click on the pattern in your swatch panel to reach the pattern options panel.

Transparency Mask

• Put a white map on the background at the same position os the used map


• Make the lines


• Select the used map and the lines


• 
  Transparency Panel > Make Mask
  


• Uncheck Clip