well If you went to a strore and asked this you would be perceived as very rude. (If you do not feel like using Pan, you can always use plurals in shop,)

but you are right that while 'your" is implied, it is not stated, so I think answer without is should be accepted.

Obviously both pants and trousers are accepted. That is I think one of the most absurd differences between BrE and AmE - 'pants' mean 'underwear' in BrE and 'trousers' in AmE. Duolingo, as an American company, rather favorizes American translations.

My first thought is: "You were supposed to wear (or at least 'to take') short pants, where are they? I don't see them, do you have them in a bag or did you leave them at home?".

Second thought: "Where in your house do you keep your short pants?".

"Where do you wear them" - nope.

"Where in the store can I find them" - maybe. Not with "masz", unless your friend works in the shop so you can be that direct with them. Plural "macie" is more probable, but not exactly polite. "Gdzie mają państwo krótkie spodnie? (Formal You, plural, mixed) is okay. Mixed is most probable because you'd rather refer to the shop rather than some specific people - although if all the staff you can see is of one gender, then perhaps panie/panowie would be fine.

'pants' to plurale tantum, czyli rzeczownik(noun) który występuje tylko jako liczba mnoga, a w liczbie mnogiej nie używamy przedimków nieokreślonych(indefinite article) w języku angielskim.

'Where do you have short pants' prawie na pewno jest tu akceptowane. ;)

"where are" works.

Oops - just looked at what i typed again. Looks like it came out as "we are" rather than "where are".