“it confused me because there are still 4 letters, not 3 in අනත්ථ ..”
No. The last two are combined and are counted as one.
“My end goal is to learn the correct Sinhala script for the 3 concepts anicca, dukkha, anatta.”
Those three words are written in Sinhala script these days as: අනිච්ච දුක්ඛ අනත්ථ (or අනත්ත).