Use of conditional sentences

The most grammatically correct tenses to use in this sentence are

If the trekkers had chosen a shorter route, they would be in trouble now, but fortunately they didn't.

That is because we are dealing with two different time periods — they chose their route in the past, and they are (not) in trouble in the present — so you need to use what ESL classes call a "mixed conditional". The tense you use in the "if" clause for past hypothetical conditions is the past perfect, and the tense you use in the main clause for hypothetical situations is "would + bare infinitive".

Having said that, let me add that it is very common in English to use the past instead of the past perfect if the context makes the sequence of events clear, so the following would be perfectly acceptable most of the time (although possibly not on grammar tests):

If the trekkers chose a shorter route, they would be in trouble now, but fortunately they didn't.

Finally, if you replace "would be" in the above sentences with "would have been", they are perfectly understandable. But they don't sound as good to me.

In comments, Edwin Ashworth wrote:

• If the trekkers had chosen a shorter route, they would have been in trouble now, but fortunately they hadn't done.

is accurate but a little formal and wordy.

• If the trekkers had chosen a shorter route, they would have been in trouble now – but fortunately they didn't.

is arguably less felicitous as regards agreement of time-staging, but is punchier and quite acceptable. (I've switched to a dash because I prefer to distinguish the subtypes of comma; also, the longer pause makes the switch from past perfect less incongruous.

Zwicky, I think, stated that more padding in a sentence usually makes incongruities less recognisable, and the whole sentence more acceptable.

I would prefer the first version. However, if they had chosen already suggests that they didn't, so the second part of the sentence is rather redundant. You could say '...but fortunately they went by XXX route.'