The quick answer to your question is YES. There are definite benefits to fitting a low-restriction muffler to your diesel.
When I did so on my Mazda B-2500 pick-up both the fuel economy, acceleration and top-speed improved considerably over the stock muffler.
Just be careful in the selection of the muffler. It should have just enough restriction and not be too free-flow, or else torque and economy will be affected. Balance is the key word.
I trust just one person in this, Mang Tony Sison of Sison-Mercado Trading (SMT) of Mascardo St. Makati. He's a little pricey but the quality is second to none. Tel is 896 92 43.
Ask for a turbo-type muffler and resonator (with the same diameter as your existing pipe). He'll know what to do.