I can't quite grasp this problem. I'm not sure that the timer has a great deal of impact on the situation, although I tend to play many hours per session, so maybe it's a problem I have no frame of reference for.
I use the "per hour" thing as a way to compare profits, because of course you can't really decide whether a billion-credit profit is worthwhile without knowing how much time it takes to make that billion. A full hold of smuggling missions could be taking as long as 3 hours to collect and complete on average, depending on more factors per player than I can think up, but the cr/hr is meant to indicate how much you might get at best per unit of time spent; you don't necessarily have to spend any particular length of time at it to make it useful.
The shortest mission timer I've seen thus far has been ~1.5 hours, so I might prioritise that one, but more often they're so forgiving that I can forget about them and just go about it at my own pace. Having 45 minutes to land at a place and click a button, especially when you're being chased there, does not seem very tight (assuming we spend 45 minutes waiting on more missions before departing).
Additionally, I've been caught smuggling the mission cargo probably 10ish times, and have had to abandon one that I misread. They don't seem to mind in the least, and I've ended up allied with 2/3 of the issuing factions and friendly with the rest in the process. I expect outright losing the cargo for 8 missions at once might set my standing with them back to square one, which seems to mean that they'd go back to giving me slightly fewer millions of credits.
Do tell me if I'm wrong, I feel like I'm misunderstanding the points made here.
Edit: I also want to re-mention the huge trader ships coming in 1.5. I expect 1.5 profits to dwarf the pre-1.4 profits in yet another way, so this all might be small potatoes.