Hmm, I know this is kinda late but I figured I should give my two cents since I just picked this game up again.
To the op question: I would just land at the first one, abort, then land at the second one and complete. If it is a cruise mission then just skip it- not worth the effort. Then again, your ship might not be able to redirect after aborting a mission (I've only done it once in my current campaign- veteran) so be aware of that.
Hammerheads and Leviathans are great but remember they require Zrbite for fuel. In my past games Zrbite was a huge limiting factor and I got sick of raiding ships for it. You're better off keeping a Barracuda around for small ships and Tritons for basic transports/detectors. In fact, the first thing I did when I started my game was sell a Barracuda and buy another Triton. With the fuel cost of Zrbite I might consider not even using new subs for combat and sticking with barracudas.
For fighting lobstermen, I've only abandoned one mission and that is because I forgot to bring a thermal tazer. Don't get me wrong, it is still completable if you have gauss/sonic but it is VERY painful. Since I don't save/load my games (other than in the beginning for backup), a lobsterman terror or landed craft would likely wipe out half my crew. Even with tazers they take like 2 shots and it's expensive with TU's so unless you have lots of rookies to spare go for Vibroblade or get MC before fighting lobstermen. The current technique I use which works great (before MC) is to thermal shock them and then throw one grenade. Live unconscious aliens die immediately if any explosions go off near them. I don't even use Sonic cannons because of the TU penalty and also because they are great to sell. However if you don't loot the bodies before you kill them you lose a lot of valuable loot! Maybe you could pile the bodies and create a lobster bonfire.
Wow I'm typing too much!
Okay lastly I'd like to say that base assaults are really not worth to complete via killing all the aliens. It is a PAIN PAIN PAIN to kill all enemies in the 2nd mission, and unless you are a save/load whore you are bound to get stung by a tentaculat and possibly lose your best guys. I did one recently to see if I could get massive Zrbite but it took 3 hrs to complete the mission and I lost my best soldier in the process to the last tentaculat. The result? 5000 pts, Tons of cash in loot, and 70 dead aliens. I did it without using tazers or medikits. Would I do it again? No way! I've beaten this game 3 times and only finished 2 base missions and by the end I'm just exhausted. There was no Zrbite in the end so totally not worth the risk unless you are far behind in pts/cash.
One more thing... medikits aren't really worth it IMO. Early on I just manufacture particle displacement sensors to make money. I used to arm each person on my team with a medikit but now I just bring 2.