Many commented on "is it negative impact", I want to write a short reply on "maximizing positive impact" (assuming you care about this; if you don't then ignore this) :

TL;DR: What's your main reason to think that working there will lead you to a high impact career? 

• Is it that you'll learn a lot there? 
• If it's the direct impact (from the battery and energy services), then my prior is that you'll have a much higher impact working on an EA vetted org (vaguely defined. But basically an org that was found by you or others to probably be one of the highest impact ones in the world).
• Or maybe it's something else, like "you have friends there" or "it's the building right near you" 

A few thoughts, though I wouldn't give them too much weight:

The considerations I can think of look something like:

(1)Sonnen does work with some positive externalities.

(2)Sonnen makes some profit, which either goes to Shell shareholders, net of taxes, or might be used to finance other Shell activities.

(3)Shell might be able do other things with negative externalities and suffer fewer consequences due to positive PR effects from Sonnen.

Since Shell will probably evaluate other projects on their own merit, and can easily borrow money in financial markets, (2) probably doesn't matter, I think. Shell shareholders are basically just the same shareholders as every other big company.

I have not much idea how much good there is in (1) versus bad in (3), mostly because I know little about (1). I would be a bit surprised usually if second order effects were larger than first order effects.

Also, I think a world where Shell wants to invest in clean energy projects is better than one where it doesn't. If those projects do well then that might mean more spending goes to them vs other projects, more because of limited management capacity and better PR rather than not having enough money to do both things.

If there were two otherwise identical options I'd probably lean towards the non Shell option, but I'd guess this factor should probably not overwhelm a substantial difference.

What do you think Shell will do with the marginal additional profits?

If it distributes to its shareholders, then Shell is just acting as a pass-through entity and the profits issue doesn't seem different than if the shareholders owned sonnen directly.

If you think Shell will invest profits back into its businesses, a lot would depend on which business the marginal investment went into. One could argue that a successful sonnen would motivate Shell to invest more in greener technologies.

As you note, there are issues other than who gets the profits.

I've thought a fair amount about this (Shell recruited pretty heavily at my college). I agree with previous answers and think those are probably the primary considerations. Some other thoughts, both for you personally and on the moral value of the work:

• Being thoughtful (as you are doing) is half the battle, and it's key to make sure that your own values and motivations aren't led astray by the environment you will be in - it's easy to have value drift when your job is on the line. 
  • I wouldn't underestimate the subtle ways in which being owned by a FF can change the way a company does business (and therefore what you are able to do and what you are rewarded for). An imperfect analogue is the way SBF's funding shaped what EA orgs did over the past few years, and the resulting fallout and instability now.
    • There's some research that even if you have idealistic motivations about doing good, the environment around you can shift your preferences towards whatever is externally rewarded, e.g. here re law school. 
    • It is hard to be motivated and do your best work (and therefore get promotions, transition into a better job in the future, etc) when you don't feel affirmed and aligned with your work.
• There is utilitarian value in socially stigmatizing fossil fuel companies. If FFs (& the companies they own) can't find talent, that's yet another signal that they should be seriously re-evaluating their business model. I do think this consideration is less clear when it comes to acquisitions like sonnen.
  • If you care about what climate people think, there was a lot of discussion on Twitter recently of a similar piece in NYT's The Ethicist (though I personally disagree with climate Twitter consensus on this).

I wouldn't do it myself in your situation, especially since there are probably plenty of non-FF-owned clean tech companies hiring SWEs. But it's not clear to me whether it would be net good or bad, for the world or for you.

I haven't thought much about it, but it seems reasonably likely that your straightforward line of thinking is correct. 

In particular, things like:

• Improvements by sonnen which could threaten Shell's bottom line would be much less likely to happen, but might be the most valuable
• sonnen might not aim for large-scale expansion
• as you say, it might be used to greenwash Shell

I think it's a consideration, but not a strong one. The company existed before being acquired by Shell, so the value of their work is not dependent on this. Shell is for sure using them for greenwash, but does your working there actually matter? Maybe, maybe not. I guess it would be more difficult to be motivated to make the company succeed when you know of these additional consequences of success.

It also matters what your alternatives are.

You don't know yet how Shell's ownership affects what Sonnen does in the marketplace. If you think home batteries are a net positive morally then it's just a matter of comparing the impact of Sonnen with the impact of other companies where you could work.

Home batteries are part of the energy transition at small scale but I don't believe they matter at large scale in terms of reducing climate destruction. However, home batteries are great for buffering against blackouts and if I were a homeowner, I would be grateful to have a battery technology like Sonnen's.