Etymology: ע used to be pronounced differently (and some people still pronounce it differently). So it's like asking why we write "year" instead of "yeer": it used to be pronounced as "yay-arr" but not anymore. Although it's different, because some people in Hebrew still pronounce ע as it "should" be.
Also, it wouldn't be ים, it would be אים because you need the א to show that the י is pronounced as a vowel and not as the consonant y. ים is already a word: "yam" - sea.
The word for "if" is אם, also pronounced as "im". Theoretically it would be spelled אים but it's such a common word, no one includes the י.
The words אם and עם sound the same for most native speakers but different for some Arabic speakers (whether they're Christian, Muslim, Jewish or Atheist...).
I was taught by a classical Hebrew professor to pronounce ayin gutterally, in the back of the throat, as he pronounced it, but he was obsessed with proto-Hebrew and diachronic aspects of the Hebrew language (how it changed over time). Modern Israeli Hebrew, from what I can tell, does not do so, as you indicate, except for those trying to emulate the past. From what I can tell from DL pronunciation and the Israeli tv program סרוגים, the kaf is pronounced more as a ח than a ח! The latter is more like a harder ה.