English is indeed a strange language with lots of exceptions to the "rules," as you have noted. I suppose this is due to the historical development of english from a wide variety of outside languages, including , french, german, norwegian, etc.
In learning phonics as children there is a lot of emphasis not just on the sounds of the 26 letters but also the special rules for diphthongs - that is, special combinations of letters that together indicate a particular sound. You point out "tion" sound like "shun." "Sh" is itself a common dipthing - it certainly doesn't sound like "s" and "h" separately. Another common one is "th" as in "the" or "both." You just have to memorize what the various dipthings sound like, as well as the individual letters. One of the most confusing is "ough" which may sound like "off" (as in "cough"), or like a long "O" (as in "though") or as "ow" (as in "bough"), or "uf" (as in "enough").
As for silent letters - an ending "e" helps identify that the preceding vowel is to be pronounced using the long sound - for example, "mope" versus "mop." But as to why we have silent letters like the "h" in honest - I don't know.
It amazes me how so much of the world has managed to master all this!
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