Say Mew ex used its "Genome Hacking" attack last turn to copy Sylveon ex's "Angelite" attack. If I use "Genome Hacking" this turn to copy the same attack, can I shuffle 2 of their Benched Pokemon into their deck again?

Yes, you can. Mew ex used "the effect" of Angelite last turn, but the "attack" it did was Genome Hacking, so the restriction of Angelite does not apply.

Relevant cards

SV8_86

SV35_151