Even native plant gardens need maintenance. All too often I see native plants advertised as "low-" or "no-maintenance". Although it is true plants native to your area will require less maintenance than conventional, generic plants (that is, those not suited for a particular climate or locale), they do require some maintenance in a garden setting. As I often remind people, it is "xeri-scape" not "zero-scape".
Inherently, periodic care, cultivation or just maintenance defines a "garden" and distinguishes it from a natural area. Perhaps instead of "maintenance free", native plant gardens should be thought of, and referred to, as "less resource intensive". This is probably a more accurate, and appropriate descriptor, since, in their native environment, native plants do not need soil amendments, fertilizers, pesticides, protetction from hot summers or cold winters, and additional water (once established), but they do require care.
I think that the lack of attention people pay to native plant gardens does a disservice to promoting native plants as landscape alternatives, especially when the aesthetic is a departure from the accepted norm. The norm being the French or English garden of a manicured lawn, and a few specimen trees. As I have mentioned in past posts (read: ranted), native plant gardens need to be thoughtful and consider the same design elements as any landscape. Having a native plant garden is not an excuse to to have an unkempt garden.
Maintenance for a native plant garden may be for a variety of reasons including: aesthetics, "tidiness", to promote undergrowth, to deadhead and prolong the bloom (though this is not very effective in our climate since we do not water), to maintain diversity of plant species and structure, or so some flowers don't set seed.
As far as letting flowers go to seed or restricting them from seeding, I do a combination. I like to leave a lot of seed heads on plants for birds, and insects but not necessarily all of them. For example, showy fleabane (Erigeron speciosus), three-vaned fleabane (Erigeron subtrinervis), and hairy golden aster (Heterotheca villosa), and others are prolific seeders, and without management they would probably end up dominating the garden. So, in certain areas of the garden I cut them back to limit their spread. However, they are easy to grow, beautiful flowers, so I many places I am not too disappointed if they take over. Others, like blue flax (Linum lewisii) and bluebunch wheatgrass (Pseudoroegneria spicata), I manage more intensively (see "What is a weed" and "Shades of blue" posts for more information).
Seeds of blanketflower (Gaillardia aristata), and many aster and erigeron species (I can't necessarily tell many of them apart), get eaten by pine siskens late in the winter. Some seeds, like balsamroot (Balsamorhiza sagittata) and narrow-leaf collomia (Collomia linnearis), get eaten almost immediately by beetles and shield bugs.
This evening I did a lot of, what I call "non-technical" pruning. I cleared out several paths (see photos above and below) that had be overgrown by flowers, and reshaped many plants to provide depth, and diversity to the landscape. To me, this is the fun part of gardening- reshaping and redefining spaces. Plus it is fun to just experiment and "putter" about the garden.