Does publishing in multidisciplinary journals undermine perceived work quality or impact? For example, Heliyon is Elsevier's multidisciplinary journal which I'm considering publishing in. Is publishing in a broad-scope journal such as this one or PLOS necessarily detrimental to one's career or the likelihood of the paper being impactful?
In Web of Science's Journal Citation Reports, there are 236 categories ranging from &quot;Acoustics&quot; to &quot;Zoology&quot;. There is also one category called &quot;Multidisciplinary Sciences&quot;. PLOS ONE is in that category (and Heliyon is still in the ESCI, so not assigned to a category yet).
If you sort Web of Science's list of categires by Aggregate Impact Factor, you will see that &quot;Multidisciplinary Sciences&quot; ranks at #10 out of 236 (as of early 2021):

Your question, it seems to me, is too general to answer properly, but perhaps this formal approach might indicate that the answer is: No, publishing in a multidisciplinary journal will not necessarily harm you. As Libor wrote in the comments, journals like Nature and Science belong to that category.
The response might be slightly different if you refer to Open Access megajournals. There are enough skeptics, I fear. But my own guess is that in the mid- to long-term, it will not harm you. The reason is the following:
Many university libraries increasingly set up bibliometric departments that analyze your scholarly outputs when you are a candidate for a research post at that university. And one of the positive indicators they look at is the share of Open Access publications. Publishing in such journals may underline your commitment to Open Science, which is a generally positive aspect. (But again, opinions may vary.)