This was addressed in the first episode of Season 2. Winn decrypts Mon-El's flight-recorder and they find that he was trapped in a region of space (known as the "Well of Stars") where time doesn't flow normally.
Winn: Now, it seems sleeping beauty on his journey from Krypton passed through something called the ... [pauses slightly] "Segara Beyal"
Kara: The Well of Stars. My father took me there once. Time doesn't pass there. So that's why he's still so young.