I think the tilde operator and Underscore are both equally cryptic and represent similar degrees of obfuscation. Tilde doesn't get much use, because it's prone to quirky behavior, particularly with respect to negative one in javascript. Gven that javascript has junk lying around like NaN, undefined, null, ==, ===, I tend to mistrust anything that isn't dog-ugly bland convention.
Aliases are also ugly in my opinion, given that they can be reassigned any old time. Even the much-used dollar sign alias demands extra scrutiny, when inspectng unfamiliar code. The advantage is that they're (aliases, that is) are easy to write, not easy read. On the other hand, the "contains" function should adhere to the sanest contract most would expect from it, and if it does, "contains" is easy enough to understand. But yeah, depending on libraries is either laziness or bullshit, when it comes to core language functionality. The only thing advanced libraries really offer is cross-browser compatibility.
Meanwhile, (x.indexOf(y) == -1) is dead simple, as long as you know that arrays start at zero, never have negative indices, and that indexOf() returns a negative value when the argument isn't matched by an object in the array. Returning a negative value, as parlance for "not found", when an absolute integer value is expected, is a pretty sane convention.