We should lean toward checking medium pocket pairs on paired boards to control the pot and bluff-catch future streets.
Checking is the preferred play here. While we have a solid made hand, betting 99 into a paired board often isolates us against better Tens or trips while folding out hands we dominate.
Note: Betting here is thin; checking allows us to realize equity and keep Villain's bluffs in.
Checking back is mandatory. The Jack is a poor card for our range, and our hand has now demoted to a pure bluff-catcher that cannot stand a raise.
Calling is the correct play. Despite the flush completing, the price we are getting is too good to fold a hand that unblocks all of SB's missed straight draws and air.