Tiny explosives are certainly not the sort of inherently indiscriminate weapons ICRC refers to. You might want to read the article you linked to, which uses nuclear weapons as the main example. The difference in energy released by Israel's beeper vs a modern nuclear payload is at least 10 orders of magnitude.
ICRC is not really claiming that those examples are indiscriminate, they're giving examples of weapons that might arguably or sometimes be considered indiscriminate.
Some booby traps might fall into that category, but this isn't a toy or a banana, it's a device specifically issued to enemy personnel.
There can be separate textualist arguments about Israel's operation based on the specific language of CCW, but that's unrelated to the customary IHL you linked to.
