The point of consonant intervals (of which chords are mostly comprised) is that the various frequencies are in a ratio of small numbers. Now if the intervals are perfect intervals, the result is a combined signal that has the frequency of the greatest common divisor of all contained frequencies, reminiscent (after frequency separation in the inner ear) of a lower frequency with a particular overtone composition.
Now the most transparent reception occurs when the virtual fundamental frequency is actually in the hearable range and most of the purported and their real overtones are in the most trained and discriminative part of the hearing, namely in the meaning-carrying frequencies for human speech, the vowel formants.
That explains why there is a preferred range for chords to be in. However, the perceived muddiness also very much depends on the instrument in question. Upright pianos suffer quite a bit from "disharmonicity" in their lower range, making even single low notes sound muddy. A guitar is written one octave higher than it is actually played, yet guitar chords tend to maintain character reasonably well for chords not written all that different. Similar for organ pipes. Low chords with organ pipes or large recorders tend not to sound muddy as much as hollow since they not just have rather pure overtones but also comparatively few of them.
But even instruments like accordion or harmonium which have numerous but pure overtones tend to work better with chords than upright pianos. Grand pianos with their comparatively longer strings and thus lower disharmonicity tend to behave more gracefully when venturing into the lower ranges.
So basically there are both rather abstract psychoacoustic reasons for the muddiness of low chords as well as some instrument-related causes depending on the instrument's overtone composition and disharmonicity.