First, not all low bridges are marked. Period. Maybe they are on interstates and most main roads, but not always. Maybe the sign got stolen. Maybe it got hit, etc. But they are not all marked.
Second, get the Rand McNally Trucker's Atlas. All roads that are safe for the 13'6" tall trucks are highlighted in yellow. Just stay on those and you'll be fine. It also has a state by state database listing low bridges. Texas wins. There are two versions of the atlas - printed and laminated. I got the laminated one mostly because it will last longer but also handy to use a dry erase marker to plot out my routes. Got mine at Love's.
I also have the Allstays Low Clearance app on my phone which is great.