What data or which data?

Which generally suggests a set of possible options, but what, on the other hand, allows for arbitrary selection. Additionally, your current consideration of data as singular is fine; however, you will need to pair it with a quantifier, as in data-set, if you intend to opt for the "choice from possible options mode".

Hence I suggest one of the following.

Which data-set is used by the model combinations?
What data are used by the model combinations?

The former asks which of a few choices in data-providers are being used, the latter asks what data-points, chosen from any in existence, are being utilized.

Again, the reason for the first sentence being singular and the second plural was to match the idea of prior defined choices vs. arbitrary sample. Merriam-Webster describes this distinction as between a plural noun and a singular mass noun.