Each of these things is incredibly unlikely, each more unlikely than the last:

- it was made at all! these were never common. multilingual cultures have always been common or even the norm but for various reasons decrees and monuments tend not to be.

- it's in languages that remained in wide use after, and of interest to a broad swathe of historians and linguists today.

- it was preserved in a usable form; it was moved and reused as building materials, how many times must it have been almost destroyed or buried? that's the normal end for similar artifacts.

Without a similarly astoundingly lucky combination of events yeah we're stuck with just grinding away with frequency analysis and similar techniques. I'm not up to date on the indus valley script but I think a stumbling block there is you have to have at least a good guess what you're looking at before frequency analysis starts to work.

We don't know what the "atoms" of that script are or what its purpose was. Are the marks similar to words, or letters, or like strokes in chinese, or like dots in braille? Is it even a writing system for a language? it could be musical notation, court shorthand, stage directions for religious ceremonies, complex tally marks for trade inventory, etc. It's probably not but that indicates the problem space a little.