I assume that by "silent letter", you mean a letter that does not ever correlate with anything in pronunciation, though the s in pas is not silent by that standard (pas encore). The k of knight would be an example. The reason in that instance is that there used to be an actually-pronounced k in the word (knight was not the same as night), some time around the 18th century. Similarly, a number of words in Spanish have <h> which doesn't indicate anything about contemporary pronunciation. There used to be an h in hechar, but it was deleted (and then some dialects re-invented [h] from [x]).
In Italian, you don't really "read each letter". For example, ogni is pronounced [oɲi], and you don't first pronounce g then n. Instead, some of the rule of pronunciation involve sequences, so the sequence <gn> has a special rule, likewise <schi, sci>. Such rules of combination explain why in Swahili the single sounds ð,γ are spelled <dh, gh> – basically because there are more sounds in Swahili than can be directly represented with singly Latin letters. In Shona, they faced a similar problem but used an extended alphabet with phonetic symbols like <ɓ, ɗ, β>, but that was unpopular so they reformed the spelling system to use digraphs, d vs dh, v vs vh and so on. Another example of is the diacritic use of <n> in Yoruba which after a vowel represents nasalization of that vowel – it's thus any combination of vowel plus n, not just a specific vowel-plus-n combination. Hmong spelling likewise has a number of consonant letters at the ends of words, but those are not really consonants, they are tone-and-phonation diacritics.
The reason to not reform spelling to reflect every historical change is that people are generally very conservative about spelling, and they get offended when others don't write the same as them. I pronounce "cot" and "caught" the same, and I just had to learn two different spellings correlated with meaning and not pronunciation. The first vowel in economic often varies within a single speaker between [i] and [ɛ], and nobody wants to be forced into a pattern of chaotic spelling just because a word has two or more pronunciations. However, you do find marketplace-acceptance of alternative spellings such as lite, nite, rite which somewhat regularizes English spelling.