The Jokers added to the deck in this case would be useless/junk cards, not wilds¹.
My intuition is that there would be no impact to how we'd normally calculate the possible combinations/frequency for each standard Poker hand, though this would add new mixes to the total number of all possible hands and thus decrease the overall probability of each standard poker hand due to the now increased total combination pool/denominator.
I believe this is because the number of possible combinations for those specific hands still remain the same regardless of how many additional exotic cards you'd add to the deck if the exact definitions for those hands aren't altered, i.e. even if there were a baker's dozen Jokers added, you still could not have a Joker Flush since a standard Flush would still be defined only from the original 4 suits and 13 ranks, which in binomial coefficients (already excluding Straight Flushes) would still be C(4,1) suits to work with and C(13,5) ranks to choose your 5-card hand from.
The only thing that'd change from including Jokers is the addition of new hand combinations that would add to the total number of all possible hands, bringing that binomial coefficient C(52,5) to C(54,5) assuming the usual 2 Jokers that come with most decks. By increasing the total number of all possible hand combinations, we have effectively reduced the overall chance for each standard poker hand by increasing the total denominator, but the actual frequency/numerator for each hand is still the same I believe, or am I missing something since my gut still has some doubts on this?
Bonus Question: For the earlier example of a 'Joker Flush', if we were to count this specific type of Flush as an entirely new, distinct kind of hand, I believe it'd simply have a total frequency of C(13,5) assuming 13 Jokers added to the deck and no straights if Jokers are just rankless junk cards?
Thank you for your time and consideration on my errant curiosity.
¹ In researching this question though, I did find an interesting article about this kind of problem but with Jokers as Wildcards which opens up an entirely different kind of question: Gadbois, S. `Poker with Wild Cards - A Paradox?' http://www2.denizyuret.com/ref/gadbois/gadbois96.pdf