Jason,
Your not alone in noticing the deterioration of the Potomac as a smallmouth fishery. I've fished it for about a decade and typically do a half dozen trips to tribs like the mainstem, North and South Forks of the Shenandoah a year as well. It WAS different a decade ago. There are simply less smallmouth in the system for a number of reasons but namely climate change.
Recently, MD stocked 30K smallies to aide in spawn recruitment, but it won't stop the effects of climate change that has produced more high water events in the last few years that have resulted in dramatically lowering the fish population in the Potomac (not just smallies).
"Several consecutive years of high river flows during the spring have reduced spawning success, causing lower catch rates for anglers. Elevated spring flows experienced in 2016-2018 have resulted in consecutive years of poor recruitment and low year-class strength. While the number of larger adult smallmouth bass has remained steady, there are concerns about declining catch rates after multiple poor year-classes of young fish."
Furthermore, I'll bet that when you floated the Juniata the one thing that you saw quite a lot of (especially closer to the confluence of the Sus) was aquatic vegetation and including stargrass. Cast over stargrass on the Jun and you'll get bit by a juvenile during topwater season on every cast. Dead drift a hopper or popper over a deep hole and you'll move an old big smalljaw for sure...but not so on the Potomac. The successive flooding of the Potomac has not only kept the smallies from spawning very well in the last 5 years, it has also SCOURED the vegetation where smallie (and other fish eggs) get caught that become nurseries. Basically, the lower Juniata is a smallie nursery. The tribs to the Potomac are suffering from the same flooding closer to their confluences on the plains with the Potomac as well. Higher elevation areas on the North and South Fork of the Shenandoah drain quickly and gullywasher rain events do not always remove the vegetation, they also have more ledge to protect juveniles. That ledge on the forks runs perpendicular to the river across a smaller width. In addition, some smallmouth migrate (not all, not even most) during the winter a few miles and so under stress they may not be found in the same places as the previous year. They also AGE slowly... a 20" 4-5 lb smallie could be 15 - 20 years old.
When you add up the impacts of climate change and the rain events, the lack of vegetation and recruitment, length of time it takes for a smallie to reach maturity and trophy size, you can easily see it could be a DECADE before the Potomac fishes like it did a decade ago with heavy stocking (and providing the rain events don't get worse...and fat chance that won't happen).
Sadly, even the Juniata isn't free from these impacts.