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Half of them. Which is still useful in biological samples that have billions of copies.

Yeah, you can still assemble a genome even if strands are broken. In fact this is done all the time as the size of the strands going into DNA sequencers are often only 100s or maybe 1000s of basepairs.

half life generally means that within the time frame 50% of the material will have been destroyed or changed.

so it would mean that half of the dna might still be available after 1M years

To be meaningful, half-life needs a Markov assumption, i.e., that the past and future are conditionally independent given the present. Or, more simply, at each instant, forget the past and for predicting the future use only the present.

Some interesting work in the many contexts where half-life works would be to say what the Markov property says about the mechanism of the decay or whatever are trying to predict in the context.