As an avid collector of vintage hardware and one who runs a YouTube channel dedicated to teaching people about how the hardware works, and how to actually use it, I can say confidently that yes, we definitely struggle.

There are a great number of games that cannot be played by most 16-bit and 8-bit console emulators. The Famicon disk system, for instance, is a real struggle to get working right.

90s machines are dying off rapidly, and hardware is becoming very very scarce. Much DOS software, for instance, requires very specific hardware timing and behaviors that is either not known about or still emulated wrongly. Worse, some emulations simply don't exist or are very difficult to get working (see also 3DFX Voodoo3 8-bit paletted textures).

2010 machines are next on the chopping block. Though tose systems may be easier to deal with hardware wise, emulation will still be a challenge.