No ideas why Czechs decided to use j for "short i" consonant sound. Poles apparently did that because they use letter "y" for another sound, which is equivalent to Russian "Ы".
The letter "j" was first invented to represent the short i sound. It is used for this purpose in many Germanic, Slavic and other languages. Letter "y" was invented to represent Old Greek sound "y" (like French u) and is used for this purpose in German, Swedish, Norwegian.