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Each ‘%’ element will be replaced by some string or other when the buffer in question is generated. ‘%5y’ means “insert the ‘y’ spec, and pad with spaces to get a 5-character field”.
As with normal C and Emacs Lisp formatting strings, the numerical modifier between the ‘%’ and the formatting type character will pad the output so that it is always at least that long. ‘%5y’ will make the field always (at least) five characters wide by padding with spaces to the left. If you say ‘%-5y’, it will pad to the right instead.
You may also wish to limit the length of the field to protect against particularly wide values. For that you can say ‘%4,6y’, which means that the field will never be more than 6 characters wide and never less than 4 characters wide.
Also Gnus supports some extended format specifications, such as ‘%&user-date;’.