What's the Real Problem?
Now, technically, you're talking about digging here, but you mention that your players ignore deadlines.
It's not that hard to make digging hurt; you can set up wherever they dig into to be more or less equivalent to the gatehouse they would storm if they went in the normal way, for instance.
However, what you seem to really be having issues with here are players that want to focus on interesting exploits, rather than traditional narratives.
Now, this could have its own issues associated with it: players could want a different genre, or feel that this is a way to get agency that they aren't getting through more traditional applications of their character, but I'm going to go ahead and assume that those aren't the issues.
Make Time Matter
You mentioned that your players blow off timelines. Don't let them do this. Now, obviously you can't force them to do stuff; teleporting them into a boss fight with the dude what needs killing is only fair or interesting once or twice tops, and you need a fair deal of setup to get that to work. Likewise, having the objective they need to complete come to them is going to be problematic as well.
With the tunneling thing, there are tons of things you could do to remove the tunneling, but this could lead to other exploits. What if the players are content to summon giant eagles and bombard the fortress with boulders?
If they don't meet the deadline, the quest fails. They don't get a reward, because the reason they were sent to stop the guy has already become outdated. Either the BBEG's plans succeeded, the quest-giver died at the hands of an assassin, or they simply get scolded for taking too long.
One thing you mentioned is that your players are used to a very brutal DM who just killed them a lot. You need to make clear that you are not that way. You can suggest things like Schrodinger's Dice, where players roll for their characters' deaths in secret and are never challenged on the dice: if they go down in a fight they'll be alive unless something finishes them off (if they desperately want it enough to cheat), and you control the bad guys so they won't be finished off.
Someone in comments mentioned the Same Page Tool; there are a lot of other ways to do this, but basically have a heart-to-heart with your players and mention your concerns with the group's planning. It may turn out that they like shenanigans like this, and then you have to decide whether or not to allow it or to encourage them to move away from it.
Emergent vs. Scripted Events
One thing to consider as well is the nature of the game: role-playing games offer an incredible amount of flexibility in actions and storytelling, and emergent play (in which outcomes are based on freely selected actions) often is a result, as opposed to scripted play (in which outcomes are based on a limited selection of actions).
Talk to your players, and ask them if they'd be fine playing more genre-traditional strategies. If not, recognize their emergent play and make it part of the setting. Enemies learn from their mistakes: if the characters let their secrets slip, or let any of the BBEG's minions survive to tell the tale, every villain they encounter has planned for their schemes. Let them know this: each strategy only works once.
Part of this is pushing the deadline. If the villain knows they'll take fourteen days to tunnel into his fortress, the appropriate response might mean setting off the doomsday device on day seven. Be fair with this, of course, and make sure that the players know that there is urgency. Heroes can say no to the mission parameters: they're not typically soldiers (though if they were you could throw insubordination at them) of the crown or anything like that, but they can't say no to harsh realities of their enemies' victories.