js 5

const ruArr = ['а', 'б', 'в', 'г', 'д', 'е|ё', 'ж', 'з', 'и', 'й', 'к', 'л', 'м', 'н', 'о', 'п', 'р', 'с', 'т', 'у', 'ф', 'х', 'ц', 'ч', 'ш', 'щ', 'ь', 'ы', 'ъ', 'э', 'ю', 'я'];
const shiftedArr = ruArr.slice(16, 32);

const table = {};
const lengthPerRow = 16;
const buildModRow = (symbolsArr, index, lenght) => {
if (index % 2 === 0) {
return (symbolsArr.slice(0, 16));
} else {
if (index === 1) {
return [...shiftedArr];
}
let k = 15;//шаг
for (i = 0; i < k; i++) {
shiftedArr.unshift(shiftedArr.pop());
}
return [...shiftedArr];
}

}

ruArr.forEach((letter, index) => {
const rowI = buildModRow(ruArr, index, lengthPerRow);
table[letter] = rowI;
})
const arrFromTable = Object.keys(table).map((letter) => [letter,table[letter]]);
//console.log(arrFromTable);

let cryptogramma='';
let key='абвг';
let message='е';
const isEven = (num) => {
  return num%2===0 ? true:false;
}
for (let i=0;i<message.length;++i) {
  //message[i]-символ сообщения
  //key[i%key.length]-символ ключа
  let indexOfKeySymbol=ruArr.indexOf(key[i%key.length]);
  console.log(ruArr.indexOf(key[i%key.length])+1)
  console.log(arrFromTable[indexOfKeySymbol][1]);
  let indexOfTextSymbol;
  console.log(arrFromTable[indexOfKeySymbol][1].indexOf(message[i]));
  indexOfTextSymbol=arrFromTable[indexOfKeySymbol][1].indexOf(message[i]);
  console.log(indexOfTextSymbol);
  if (indexOfTextSymbol===-1) {
     {
      if (isEven(indexOfKeySymbol)) {
        indexOfTextSymbol=arrFromTable[indexOfKeySymbol+1][1].indexOf(message[i]);
       console.log('two');
        cryptogramma=cryptogramma+arrFromTable[indexOfKeySymbol][1][indexOfTextSymbol];
      } else {
        indexOfTextSymbol=arrFromTable[indexOfKeySymbol-1][1].indexOf(message[i]);
        console.log('three');
        cryptogramma=cryptogramma+arrFromTable[indexOfKeySymbol][1][indexOfTextSymbol];
      }
    }
  } else {
      if (isEven(indexOfKeySymbol)) {  cryptogramma=cryptogramma+arrFromTable[indexOfKeySymbol+1][1][indexOfTextSymbol];
  }   else { cryptogramma=cryptogramma+arrFromTable[indexOfKeySymbol-1][1][indexOfTextSymbol];
      }
  }
  console.log(`${indexOfKeySymbol}  ${indexOfTextSymbol} ${message[i]}`);
 // console.log(ruArr[ruArr.indexOf(key[i%key.length])]);
}

console.log(cryptogramma);