There are several stereo options for Honda's. Does you stereo have a knob that you rotate or a toggle switch that you press upward or downward to adjust the radio volume? If it has a knob that you rotate perhaps the knob is broken and doesn't rotate the spindle in the radio that adjusts the volume. Pop off the knob and see if you can rotate the spindle and see if the volume now adjusts.
If this doesn't work call the Honda dealer and ask if they have seen this problem before perhaps it is in the radio itself.
There are people that specialize in repairing factory installed stereos, perhaps call these people and see if they have seen this problem before. I have attached two of these companies websites
Same problem 98 Civic. De-soldered "incremental mechanical rotary encoder" but all that is stamped on back is ALPS Japan. NO PART NUMBER! Five pins - 3 one side, 2 opposite side. The "2 side" N.O. still functions. Volume (3 pin) does not. OH also two anchor pins de-soldered.
Found ALPS part but unsure of electrical values. One co. in China for $1.90 plus $234 for shipping!