Are journal papers really viewed as strictly inferior to conference papers in Theoretical Computer Science? To give a bit of context, I graduated 1 year ago from an undergraduate where I double majored in Math and Computer Science and I am planning to apply for a CS PHD this coming year with a focus on theory.
During my undergraduate studies, I worked on a project with a Professor that lead to a publication in a top Information theory conference (although the paper was about an information theory problem, it was essentially a theoretical cs paper). In addition, we added a new results and submitted the result to a top information theory Journal and we got the paper accepted. The last &quot;breakthrough&quot; came when I was able to come up with a new optimization technique that was interesting from a CS theory point of view, which led to a CS theory paper.
However, after writing the paper, my advisor told me he would prefer to submit the paper to a journal (&quot;Theoretical Computer Science Journal&quot;) right away, rather than to a conference.
I understand that in CS, conferences are generally preferred to journals, but my question is, assuming that the CS theory paper gets in, would I be disadvantaged during the grad school application process against someone who has, say a SODA, paper? Are journal papers really viewed as strictly inferior to conference papers?
I understand that in CS, conferences are generally preferred to journals

I disagree: Conferences are preferred for earlier, smaller results, journals are preferred for more mature results. Journals can be considered more prestigious, given that journal articles are typically derived from earlier conference papers and are subjected to more scrutiny, e.g., multiple rounds of review (conference and journal reviewers) and discussion (after talks, for instance), and they've survived some test of time.

my advisor told me he would prefer to submit the paper to a journal...right away, rather than to a conference.

Your advisor is confident that the paper is already sufficiently mature and the typical conference-journal route isn't appropriate.

assuming that the CS theory paper gets in, would
I be disadvantaged during the grad school application process against
someone who has, say a SODA, paper?

I'd argue a journal article is superior. However, the turnaround time for a journal article is longer than a conference paper, so you might be in the position that your paper is under review, whereas a competing grad school applicant may have had their conference paper accepted. An article under review at a top journal is a good sign, but an accepted paper at a top conference is perhaps better for an evaluation committee - a bird in the hand is worth two in the bush.

Are journal papers really viewed as strictly inferior to conference papers?

I don't believe they are, but I don't think there's an absolute consensus.