Answer by MajinAkuma in this reddit comment:
In the case of Higurashi and Umineko, I‘m sure the anime cast was
casted first and they reprised their roles for the visual novels. The
original sound novels had no voice acting, so fans wouldn’t able to
hear the characters of the first badges until the anime got released.
Same as with Fate/stay night. But in some cases, if later visual
novels got full voice acting releases on the PS2 editions, then the
new characters would get their voices for the visual novel first
before the characters appear in the anime. This happens with many
other anime adaptations where the original source material didn’t have
full voice over, like many of the early KEY VNs.
Whether or not a seiyuu doesn’t reprise their role depends on the
numerous factors, factors we might never know. The Umineko example is
probably easy to explain. Tanaka Atsuko did voice Kasumi in the anime,
but Kyrie was her primary role in Umineko. She obviously reprised her
role as Kyrie in the VNs, but apparently it was unnecessary for her to
reprise her role as Kyrie‘s sister Kasumi, so they gave her another
seiyuu to distinguish the sisters better. That might be the right
choice, since multiple Umineko seiyuus voice multiple versions of the
same characters or characters that are intended to be copies of each
other, which is why they have the same voices. Kyrie and Kasumi are
just sisters, and they don’t disguise themselves as each other like
the Sonozaki twins from Higurashi.
In Little Busters!, Tamiyasu Tomoe voiced both, Riki and Rin in the
original visual novel, but in the anime, Riki is voiced by Horie Yui
instead. Horie probably wasn‘t in the visual novel because Little
Busters! was original an eroge with H-scenes, and having both
characters having the same seiyuu in the anime might have been not the
best idea, so they casted Horie for Riki.
Here’s a funny tidbit. CLANNAD originally came out without voice-over
like other early KEY titles. The characters wouldn’t get their voices
until the Toei anime films. The full voice-over version of the visual
novel would later be released during the run of KyoAni‘s TV series.
Kuwashima Houko is, of course, the voice of Tomoyo in the Toei films,
the KyoAni TV series and in the full voice version of CLANNAD.
However, she didn’t reprise her role for Tomoyo After, which unlike
CLANNAD, has H-scenes. In Tomoyo After, Tomoyo was voiced by Tanaka
Ryouko instead. Bur recently in Kaginado, Kuwashima voices both
versions of Tomoyo: the CLANNAD version and the After version, and the
anime makes a point to treat both versions as different characters.