I offer both Paypal and direct deposit and have never had an issue with underpayment or a "missing" deposit to date.

On the rare occasion buyers overpay by a few cents due to rounding up their payment, and a few have overpaid as they have made payment prior to requesting a total prior to checkout.  (I have flat rate and calculated postage on listings).

When the overpayment relates to a combined postage discount I simply ask the buyer for their account details and transfer the funds back to their account, keep a credit in my accounting records for them or add another item of at least equivalent value to their package.

I guess whether or not it is a hassle is based on an individual sellers' preferences. Personally I prefer it to Paypal as I don't have to pay Paypal fees and have the funds in my account immediately.