It has been my experience that compatibility has gotten much worse as the number of available gears has gone to 10 and beyond. There seems to be plenty of availability from distributors and retailers to support older bikes, just not at the higher quality levels. As others have mentioned, if you want XT / XTR level components, you have to go looking in the secondary market like Ebay. Proprietary parts, particularly for suspension forks can be a challenge to source. Hydraulic disc brakes are another area of componentry that suffers from parts availability and compatibility issues. Many Shimano braking systems are not rebuildable and Shimano is not forthcoming with acceptable lever / caliper mixing and matching. There are intrepid individuals whose experiments have shown what combinations do work but a bike shop, with concern for liability, may not want to support any combinations not blessed by the manufacturer. In my opinion, the real downside for the consumer is the local bike shop can't stock everything and repair / replacement of anything beyond the most common items requires ordering from somewhere, making getting the bike back in service take even more time.
In conclusion, I would say that compatibility issues are minimal for folks who do most of their own work and are willing to use sources like Ebay to find the parts they need. Retail service establishments have some different challenges that make it simpler and more profitable for them to steer customers to newer, supported equipment. I suspect, for both shops and DIY types, the compatibility issues will get worse in the future as both e-bikes and electronic shifting proliferate.