Yes, they did. Spoiler-alert, obviously.
The Dark Side Force-user and fanatical Imperial, Brakiss, started the Shadow Academy prior to the Yuuzhan Vong War in order to train Force-capable individuals as Sith (though Brakiss himself was more of a wannabe Sith than a true one). While the New Jedi Order shut down the Shadow Academy, killing Brakiss in the process, several of Brakiss's pupils escaped, some eventually linking up with Darth Krayt's One Sith.
Two of these Sith trainees, Welk and Lomi Plo, were captured by the Yuuzhan Vong and experimented upon to create the Jedi-hunting voxyn. A Jedi strike team freed these unfortunate Sith when they attacked the voxyn-production facility onboard a Myrkr-based worldship. Lomi Plo proved herself very capable of killing Vong with Dark Side techniques, impressing Jaina Solo and Tahiri Veila. The two Sith eventually double-crossed the Jedi strike team, stealing their ship, kidnapping Raynar Thul in the process, leading directly to Anakin Solo's death and Jacen Solo's capture. Incidentally, Lomi Plo would be the primary antagonist in the post-Yuuhan Vong War Dark Nest Crisis.
Another Sith apprentice, Vergere, betrayed Darth Sidious, her master possibly after discovering he intended to replace her with Anakin Skywalker - decades before the YV War began. Vergere, who was still masquerading as a Jedi Knight whilst training as Sidious's new apprentice - she was Sidious's apprentice after Darth Maul and before Darth Tyrannus - took advantage of a mission to Zonama Sekot after a failed attempt to murder Sidious, to flee Republic space. She was still on the living planet when the Yuuhan Vong arrived, atttacking the world. She brokered a cease-fire with the Vong commander, who was horrified to realise he was attacking a liviing, and therefore sacred, planet. Vergere left as a 'hostage' of the Vong, during which she played an unknown role in Shimmra's coup and executor Nom Anorr's infiltration of the galaxy.
Vergere appears to have had little long-term motivation beyond escaping Sidious's wrath, but once the Vong launched a full-scale invasion of the galaxy she initially supported them, but betrayed her patron, the priestess Elan, upon realising that the Jedi Order was led by a Grand Master Skywalker, whom she mistook to be Anakin Skywalker. She disappeared for several months, during which she contacted Darth Vader's former apprentice and self-proclaimed Dark Lady of the Sith, Lumiya, and captured and tortured the future Darth Krayt. Krayt converted to the Sith, but disavowed the Rule of Two, which Lumiya and Vergere both believed in, and so Vergere left to concentrated on someone she and Lumiya agreed would be the perfect convert; Jacen Solo.
To achieve this goal, Vergere returned to the Vong, and tortured the captive Solo. She eventually released him and fled with him, later scrificing her own life to save his, a distinctly un-Sithlike act. This was possibly due to her own advanced age and recognition that Solo was the best chance for the Sith to return to galactic prominence. She was right, as Solo would become the Dark Lord of the Sith, Darth Caedus, after serving as Lumiya's apprentice. Verhere's seduction of Solo was complicated by her need to disguise her actions from first the Vong, and later the Jedi, which might account for the long interval between her preparation of Solo and his eventual fall.