Interesting question, non-profit operations is a massive sector with a large range depending on interest.   I previously worked a lot with international development grants and social enterprise, but  I am currently transiting to the private sector. This post is mostly written from the perspective of having worked short-term in several US nonprofits and international development. 

 I personally would frame usefulness as finding a middle ground between a cause/issue you think can make the biggest impact or is most interesting, a position you think would be a good fit, and an area that is growing.  Some things could affect which area you focus on: 

1). Local non-profit v International (and within international, humanitarian v development):  Are you more interested in domestic issues, international development, or humanitarian/crisis response?  Does your program have a particular topic or geographic focus? 

2). Type of role/issue: Is there any specific issue you feel passionate about such as health, food systems, education, etc? Is there a role in nonprofit operations that you are interested in such as fundraising from donors, state/federal grant management, monitoring and evaluation, or others?  

3). Similar to #2, do you have other background or experiences that you could blend into the thesis? Some of the most interesting projects I have seen came from people mixing previous experiences working/volunteering with research into how dynamics are changing. 
 Ex: people with data experience exploring how different nonprofits manage and use data from operations or people with agriculture/food experience looking at how nonprofits doing food aid deal with nutrition and local sourcing. 

I can’t speak as much to current domestic nonprofit issues, but my understanding is some current issues are around improving data use/transparency/privacy (particular for both M&E and storytelling), making leadership more inclusive, and incorporating digit experiences or alternative strategies into fundraising.   

Some ideas that I personally think would be interesting from a broad non-profit perspective based on my experience:

1. Fundraising - How can nonprofits incorporate online storytelling and insert themselves into current discussions to raise awareness about their issues in a way that does seem insincere or cause damage? Basically, looking at innovation from traditional appeal to emotions advertising (save a life for $1), negative virality (Kony2012), to positive effect such as how Dian Fossey Gorilla Fund incorporated a meme to raise $300k+ and generate a lot of positive free press.  A reason I think this important is that if you can respond effectively, it can widen audiences and encourage more people to donate who previously had limited exposure at a much lower cost.
2. Program Adaption - Success/failure of adaption to covid19 and how lessons learned have affected approaches to future shocks. Globally the past year+ required organizations to adapt their programming, some areas that I think would be helpful would be exploring how organizations such as food banks scaled as demand ballooned and their operations were disrupted, or how others maintained fundraising operations if they relied on in-person events to fundraise.
3. Innovation - Improving understanding of success factors in automation and scalable systems.  This can range from improving access to resources such as more automated legal aid, lower office operations cost, or developing more efficient delivery of services.  In personal experience working in a remote area of the world, I saw several groups pitching agriculture apps as the next golden bullet, crashing because they did not understand the local context, then another group would pitch the same thing 6 months later. I think building scalable systems can create massive benefits at a lower cost if done correctly but requires a good mix of determined/scrappy team, vision, and support, and this is sometimes not well understood.

Feel free to reach directly to me if you are interested in international development and I'm happy to share what I know. 

External Links:
80,000 Hours Problem Profiles: The organization 80,000 Hours has a great list of problem profiles with links to relevant research. 

The Introduction to Effective Altruism is a great post series that explains some of the key concepts in EA and might provide insight inspiration to finding a nonprofit research topic. 

The New Humanitarian Podcast: A non-EA perspective is the New Humanitarian's podcast series on the future of aid, I would skim the titles and see if any interest you as topics.

What is the legal and practical feasibility of a global DAF that could facilitate tax deductible donations from any wealthy country to any charity registered in a different country (but not registered in the home country of the donor)? Practical considerations would need to include FX risk.

Or, to put it another way, how might we build a platform to let people in India or China donate to Malaria Consortium?

One idea may be predictors of successful fundraising (ex// sector, revenue source, revenue distribution)
 

A couple of quick ideas from a legal perspective:

• How to differentiate policy advocacy (which c3's are allowed to engage in without limitations) from lobbying (which c3's have significant restrictions on) in non-US systems (e.g. in the US pushing for agencies to adopt regulatory schemes does not count as lobbying, but the distinction between executive agencies and legislative bodies may not translate well to other governmental systems)
• Effect of China's NGO law (which creates huge barriers to giving/operating in China) on high impact causes (you'd probably need to narrow this down for a 30 page thesis - so maybe choose one specific cause), and what US/non-Chinese orgs can do to work with/around them
• How the US regulations could better facilitate international giving (e.g. equivalency determination certificates should be good for a duration and not need to be re-issued for every grant, and anti-terrorism legislation should have a negligence standard rather than being basically strict liability)
• and I second Abraham's suggestion on what US orgs can do to prepare themselves for proposed DAF changes