Languages evolve. Some sounds disappear. "Enough" was once with a gh gutteral sound which no longer exists in Standard English but still is in Scottish and Irish lough or loch. In bough it is silent. In Humphrey Clinker the Welsh maid in her letters spells all the gh words with an f.
In many Spanish dialects the final s and d become silent.
A Cuban teacher is said to have warned her class, "Clase no-otros no no- comemo- la- ese-!" gobbling up all her esses, saying "Class we do not gobble up our esses!!" and proceeding to do it anyway. If that dialect of Andalucia and the Caribbean had become the literary Spanish then the s would be a silent letter in many words officially!
I believe Danish has a lot of silent d's.
Writing systems are full of inertia and take a long time to catch up with the evolution of the language.
Also, a language adopting the alphabet of a completely different language may just ignore the spelling that maintains the original letter. I believe that Persian ignores some of the letters in the original Arabic alphabet andI wouldn't be surprised if Urdu does the same. The Cyrillic alphabet used by Russian, Bulgarian and Serbian represented the sounds of a medieval South Slavic language that missionary Saints Cyrill and Methodius tried to adapt the Greek alphabet to. Some of the letter made no sense in Russian and the country had to wait for a revolution to straighten that out.