Does a zero value in innodb_index_stats.rows_per_key mean the index is over-specified?
Comparing these:

INDEX(a,b,c,d,e)
INDEX(a,b,c,d)



Each can handle the same queries (assuming that e is not in the query).
If exactly those 5 columns exist in the query, then the longer one has an advantage of being "covering".  This might give you a 2x speedup.
Yes the longer one takes more disk space.  This impacts the speed of it only slightly.  (Obviously, the impact depends on the size of e.)
There is no hard-and-fast rule saying you should stop with 4 versus have all 5.
My Rule of Thumb says "don't go past 5".