Impact of W's on grad school admissions in CS theory (TCS)
First, I strongly suggest that you talk directly with the theory profs in your own CS department.  First, they are the people who actually taught you and are best placed to understand the circumstances of your withdrawals.  Second, they are the people who make graduate admissions decisions for your department, in your target subfield.  (Third, they are the people most likely to provide you with recommendation letters, so making contacting with them early can only help you.)

Opinions on W's differ, but as far as I can tell, most people treat them as no-ops.  Students drop classes for all sorts of reasons.  Some faculty might wonder why you waited until after the drop deadline to withdraw from these classes, especially if the W's were spread over several semesters, but that would be a minor concern, especially if you retook the same classes later and did well.  But it really doesn't matter; the W's are already on your transcript.  You can't do anything about it, so you shouldn't worry about it.

COVID-19 hit everyone, everywhere.  Every graduate admissions committee still has to figure out how to make admissions decisions with a full semester of grades missing, or at least obscured by a myriad of different pass/fail and Credit/No-Credit options.  Different people and places are going to interpret this semester's (and the next several semesters') records differently, some with more sympathy and others with more strictness.  You can't do anything about it, so you shouldn't worry about it.

A master's degree is a somewhat risky option.  At least in the US, PhD applicants who have graduate experience are held to a higher standard than applicants who do not.  Students applying from masters programs are compared with each other, not with undergraduates, and considerably more of those masters-level applicants will have research publications.  To first approximation, publications are a de-facto requirement for masters-level PhD applicants.

Persistent rumors notwithstanding, publications are not a de-facto requirement for undergraduate PhD applicants, even in hot fields like machine learning, even in top departments.  Research experience is necessary to get into a top PhD program; research papers are not.  Yes, a significant fraction of new PhD students in ML have publications, but an equally significant fraction do not.  

All that said, a strong research publication is definitely a advantage in PhD applications, especially if the recommendation letters make it clear both that the work is good and how the student made it happen, and the topic of the paper meshes well with the research interests of the faculty where you're applying.  Good research results can overcome all sorts of other weaknesses in your application.

On the gripping hand, nothing in your question suggests that you have any weaknesses in your PhD application.  Your GPA is high enough to draw the attention of human reviewers.  At that point, your research statement and recommendation letters matter far more than anything else.