Learn Croatian: Vlakovi prolaze kroz duge tunele. - Trains pass through long tunnels.

The preposition kroz (through) requires the accusative case to show movement through a space. Tunel is a masculine noun. In the accusative plural, masculine nouns take the ending -e, and adjectives describing them also take the -e ending, giving us kroz duge tunele.

The verb is prolaze. Is this related to other motion verbs like dolaze or odlaze?

Yes! They share a common root for movement. The prefix pro- adds the meaning of going through or past something. So prolaziti means to pass through, just as dolaziti means to arrive and odlaziti means to depart.

Why is the plural of vlak formed as vlakovi instead of just adding an -i?

Vlak is a one-syllable masculine noun. In Croatian, most single-syllable masculine nouns get the extension -ov- (or -ev-) inserted before the regular plural ending -i. This makes pronunciation flow better.

If the tunnels were the subject of the sentence, would they still be called tunele?

No, tunele is strictly the accusative plural form. If the long tunnels were doing the action (nominative case), the phrase would be dugi tuneli.