I've started giving them Nature/WIS/etc checks to understand the situation
I usually don't even require a check of some sort.
I'm also from the "no check" school of thought. If I, as GM, think that the game might be better if the players took account of some factor that they have overlooked, then I'll just mention it. I don't see the point of making it contingent on the result of a d20 roll. Conversely, if the game can play just as well without the players having regard to the factor in question, then I don't see any need to talk about it unless the players bring it up.
As far as resting is concerned, I don't tend to run extended dungeon scenarios so the "rest or retreat" decision doesn't come up that often. But generally my players will keep going until a viable rest opportunity comes up. If they have to keep going without dailies or low on hp/surges, they will - adapting their tactics appropriately, while (to an extent, at least) relying on me as GM not to hurl assailants at them that they have no chance of beating. I find that 4e's encounter building tools are a big help for me in this department.
I dont think this was a 'Let's Rest' moment so much as a 'We didnt plan our op' moment. I am like Dannyalcatraz, I plan the extraction before and during the operation. On a good op, that means that once you get the mcguffin, it should only be a matter of running fast enough to get to safety.
This reminds me of a Rolemaster session I ran over 20 years ago. The PCs were committed to an assassination mission against the Scarlet Brotherhood's ambassador to Greyhawk. They had a good knowledge of the defences and capabilities of the other NPCs guarding the ambassador, and
they planned the assassination in great detail, including pouring dozens of spell points worth of buffs (to hit bonuses, defensive bonuses, invis, etc) onto their party ninja.
The all gathered invisible and silent on the hills around the ambassador's residence, then sent the buffed PC in to do the job. Which she did. But then the retaliation came. One of the Scarlet Brotherhood NPCs - a mind monk, whose capabilities the players knew well - started using his mind-detection spells to track down all the thinking beings in the area, and then quickly gathered his NPC allies and started hunting them down. And it was about this point that the players realised they hadn't planned their escape. And their lack of planning was compounded by the fact that they were all invisible and silent, and so couldn't communicate with one another to try and improvise a coordinated response.
It became a free-for-all, as the PCs fled, some being successful while others got caught up in combats with various of the Scarlet Brotherhood NPCs. In the end the party elementalist summoned flying air elementals to evacuate those PCs who hadn't made it out on their own, and only one PC died (the secondary PC of the player of the ninja, and the ninja's partner - he was decapitated, and had to be buried with a bust - carved from the party shapechanger sitting as a life model - in place of his head). But the episode lived on in the memory of that playing group for a long time.
The player of the ninja suffered again from bad planning a few levels later. Being caught in a combat beyond her capabilities, she decided to retreat, having the advantage of speed. She was running through the streets of a city she didn't know very well, so decided to adopt a systematic approach to avoid getting lost. She turned left, left, left, and . . . left, and ended up stumbling into the rear of her pursuers - who then turned on her and cut her down before she could escape again. (From memory, her body was returned to Greyhawk and buried with that of her decapitated partner.)