Does it matter for liability if I structure my purchase through a holding company?

Using a holding company on top of your purchasing corporation is mainly a tax and governance choice, not a way to change the liability rules of the underlying transaction. Whether you buy shares or assets directly, or through a subsidiary owned by your holding company, the liability that comes with a share purchase, or the liability that an asset purchase leaves behind, is determined by that transaction — the holding company sits above it.

What a holding company structure generally does add is another layer of corporate separateness between the operating risk of the business you've bought and your other assets, including any other businesses held elsewhere in the same group. If the operating subsidiary runs into a serious problem, ordinary corporate law principles generally keep that risk contained to the subsidiary rather than automatically reaching the holding company or its other assets, subject to the usual exceptions like personal guarantees you've signed or a court disregarding the corporate structure in rare circumstances.

Because holding company structures also affect things like future sale flexibility and tax treatment, it's worth having a business lawyer and accountant design the structure together before closing, rather than adding a holding company as an afterthought.