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1. The fill operator works on atomic values. When you try to use it between a dictionary and a string, it attempts to match up each character in the string with the corresponding element in the dictionary, so it tries to do “eu”^”n” (first element) and “eu”^”a” (second element) but there it can’t go further as the list on the right doesn’t have enough elements, but even if it did, this is not the operation that you want. Since a string is a list of characters, ^ cannot be used to fill an empty one with a non-empty one like it would be possible with atoms. So your only option is to check the length of the string and replace it if it’s zero.
2. When assigning by index, the item on the right must have the same number of elements as the number of indices you are assigning. Once again there is special handling for atoms in that you can assign them to more than one index at once, but a string is a list, so that doesn’t work. Instead you need to provide as many copies of the string as there are indices. It can be simplified a bit by assigning the index list to an intermediate variable that you can take the count of:
ind:where 0=count each myDict; myDict[ind]:count[ind]#enlist"na"
3. As explained in 1., fill works element-wise, so the 99 is expanded to match the size of the dictionary (3×3) and then every element is filled in with the 99 individually. This works because the atom can extend to any size, but lists don’t auto-extend so they must match in length.