Legally, should a company payout or hold accrued vacation/sick time while an employee is on STD/LTD?

Depends on your state regs, but absent anything at that level, it depends on your company policy.

Vacation and sick time are two very different things. Many companies don't pay out earned, unused sick time.

A safe way to go would be to develop a policy that states that all accrued vacation time (and sick, if that's your intent) will be paid out at the beginning of the unpaid portion of an FMLA-approved leave of absence. This keeps your records a little clearer. If the employee returns from an FMLA approved leave, vacation accrual begins again from the point of return.