That niqqud in the מ is called שווא נע. Probably at the time the niqqud was invented it was pronounced as a very short /e/ sound. I believe that very formal speakers (e.g. some news narrators in the radio) actually reproduce that sound, and that sounds very formal but correct. Pronouncing it without vowel at all (as implied by /mrak/) or a full blown /e/ sounds very strange and wrong to me. As said above, Hebrew speakers just say /marak/.
Well, in products made of tomatoes, the tomatoes are normally a plural noun in the construct tail, the same with מִיץ־עַגְבָנִיּוֹת tomatoe juice f.e. It depends on the vegetable, you would make a מְרַק־יְרָקוֹת vegetable soup (plural), but on the other hand a מְרַק־גֶּזֶר carrot soup or a מְרַק־דְּלַ֫עַת pumpkin soup (singular)