Runes.txt and gems.txt are not related in anyway. Runeword stats aren't related to rune/gem stats, they are saved on a special section for each item in the D2S [the same section is used for setitem stats, hence setitems cannot contain runewords] (while gem/rune base stats aren't saved at all and applied in realtime --- thus not bound to ISC). The item also stores the runeword index (from runes.txt) if a runeword is assigned to it, now the D2S is limited when it comes to storing indexes (and these limits are much lower then the limits possible in the txt files), For affixes for example (as discussed in this topic earlier), once the item gets compressed the superflous bits will be omitted. For affixes this is only a problem inasmuch as that they will lack special color and string indexes but for runewords they would transform into ITHs that get deleted the next time a game is joined.That depend how runes.txt is used. Haven't checked into runes.txt code. But, if it's handled in same way as gems.txt. This can't be the reason.
It seams unlikely (even) for blizzard to impose this limit on runeword count if it wasen't for some format restriction.
Along the lines of limits, were is the info about MonStats2.txt being 1024 records at max comming from? I've dug through so much monster code without finding reference to this that I think it was only there during the v1.10 beta.