The problem with holding MLPs in an IRA (either Roth or Traditional) occurs when (or if) you sell the units, not during the holding period. Upon sale, ALL prior deductions applicable to reduce income (depreciation, depletion, etc.) are recaptured and is considered UBTI. If you never sell the units and let your heirs deal with it, then there is no problem...for you.
IF you happen to own an MLP that DOES have substantial UBTI (and there are several), if the taxes exceed $500 per calendar year, then the IRA must file quarterly payments, or be subject to penalties.