Has the suffix "-trix" acquired a pejorative meaning in recent years?

I think it's just that the -or suffix isn't generally thought of as implying gender today (in the movie industry we increasingly see references to female actors, for example).

Effectively, there's a general tendency towards either switching to existing gender-neutral terms, or forcing the main (invariably male) form to be treated that way.

I'd also say the -trix suffix isn't really "productive" today. If we really want that distinction, we'd probably use -ess (in which context I'll just note the Collins definition protectrix = protectress)

I wouldn't give much credence to the idea that we avoid -trix because of associations with the only significant survivor dominatrix. I think we avoid the form because it's dated/archaic - but in that one particular case it's been retained because it's a very specialised context where issues of "gender equality" don't really arise. Nobody complains about the "sexist language" of Miss whiplash either!

The college I attended (several decades ago) had, instead of a "student body president," an "executor" or "executrix," depending on the gender of the officeholder. A quick Google search yields 9420 matches for executress and 1.26 million matches for executrix, suggesting that executrix remains the more common feminine form of executor.

I don't know whether the -trix ending has fallen into particular disfavor, nor whether, if so, that disfavor is due in any way to the influence of dominatrix. I do think that, in general, adding feminine endings to occupations that normally lack them (as with comedienne or poetess or aviatrix) strikes a discordant note in modern usage because such a word choice may seem to imply that the person's performance of an objectively gender-neutral role is inseparable in some way from her being female. Why should a woman with expertise in grammar be labeled a grammarienne?

The main exception to this tendency involves the term actress, which seems to carry no invidious or patronizing overtones; other words such as heiress may also qualify as exceptions.

Update (October 4, 2020): A reference work's discussions of '-ess' and '-trix'

Michael Quinion, Ologies and Isms: A Dictionary of Word Beginning and Endings (Oxford: 2002) has the following entries for -ess and -trix:

-ess Forming nouns denoting the female gender. {From French -esse, via late Latin from Greek -issa.} Many examples exist: actress, countess, duchess, enchantress, hostess, lioness, ogress, peeress, poetess, princess, waitress. In some cases it can mean 'wife of': ambassadress, mayoress. Such forms are now often seen as sexist or patronizing; many have been replaced to a greater or lesser extent by the stem term, taken to be neutral in gender (poets, for example, may be either male or female). Some examples are now mainly of historical or poetic relevance, such as abbess, goddess, priestess, and shepherdess.

...

-trix Also -trice. Forming feminine agent nouns. {Latin suffix corresponding to masculine -tor.} Though many words with this suffix have been created since the 15th century, few have been common; those few that do appear mostly now do so only in formal legal contexts: executrix (the female equivalent of executor), administratrix (of administrator), and testatrix (of testator). One that has come back into use in the latter part of the 20th century after a long fallow period is dominatrix, a dominating woman who takes the sadistic role in sadomasochistic sexual activities. Other examples, now only historical, are aviatrix, a female aviator; editrix, a female editor; and proprietrix, a female proprietor. The spelling -trice an alternative form, via French, now almost totally archaic. The plural of words ending in -trix is either -trices or -trixes.

On the -trice front, I note that cockatrice (a mythical snakelike monster with a deadly gaze) may or may not involve a feminized cock. Here is the entry for cockatrice in Merriam-Webster's Eleventh Collegiate Dictionary (2003):

cockatrice n {ME cocatrice, fr. MF cocatris ichneumon, cockatrice, fr. ML cocatric-, cocatrix ichneumon} (14c) : a legendary serpent that is hatched by a reptile from a cock's egg and that has a deadly glance.

The "legendary serpent" meaning of cockatrice seems to have originated in Middle French, not Middle Latin. The notion that the creature emerges from a "cock's egg" brooded by a reptile adds a gender-bending—if not explicitly feminine—element to the term. An ichneumon, however, is neither a bird nor a reptile but a mongoose, which, of course, is a snake-eating member of the weasel family (and not anserine in the least).

There is another pejorative influence; meretrix, meaning 'prostitute' in Latin, is the root of meretricious, meaning 'second-rate', and there are various quotations about 'the meretrix with her merry tricks'. I wouldn't say it was an important influence, but presumably it might make some people avoid the -trix suffix.