The Shluchan Oruch says in Siman 124 that if a minyan doesn’t have at least 9 people have kavanoh and and answering amen to the Shatz’s brochos, it is קרוב to a brocha levotolah.
The Igros Moshe writes in Orach Chaim chelek daled, siman 19, that if the minyan isn’t miskaven from the beginning of chazoras hashatz, it is mamish a brocha levotolah.
To get around this issue, the Mishnah Berurah in Siman 124, sif koton 19, advises for the shatz make a tanai for a tefilas nadovah, which is what I do if I daven for the amud during the week. However one cannot make a tanai for this on Shabbos and Yom Tov as one isn’t permitted to do so.
The Mishnah Berurah also writes in Siman 315, sif koton 11, that it’s assur to answer omen to a brocha levotolah.
With all this in mind, in my tzibbur on Shabbos, I’m quite sure that we don’t have at least 9 people answering omen to the shatz’s brochos. Would it be advisable to NOT say omen in order to avoid this concern?
Your point is correct, that on Shabbos the chazzan would not be able to make this stipulation. Additionally, there are others that are skeptical about doing this for various reasons. As far as what you should do, the Mishna Berura says over there that the minhag of Klal Yisroel is that we do say chazoras hashatz even though there is strong reason to assume that there aren’t 9 people concentrating on what the chazzan is saying. The Mishna Berura only says this idea as an extra, but the practical application is remains to still say chazoras hashatz.
Halichos Shlomo (Tefilla) 9 ftnt. 13, That R’ S. Z. Auerbach originally made this stipulation, however later on in life he stopped doing it, and wanted to be yotza he same way everyone else in Klal Yisroel is yotza. Also see Piskei Teshuvos 124-9 and ftnt. 91, where he brings a number of rationales why b’dieved the chazora is still considered correct even if there are less than 6 people answering amen correctly.