As a "purchaser" (end user), I have been involved in writing specs that include requirements for per-unit pricing. There are a number of reasons that organizations choose to go this route, not the least of which is the desire of an administrator (decision maker/executive) to be able to "know" what each device is going to cost. Admittedly, there are drawbacks to this type of pricing, but there are benefits as well, which can be debated in separate thread. We obviously want to get the most bang for the least buck, but not at the expense of having someone successfully win a competitive bid and not be able to complete the project down the road because they cannot afford to do the job (or do it properly).
That said, I typically expect entities bidding on projects I have managed to make a profit. Where they put that profit is up to them. Parts? Labor? Both? Having seen various companies use all of those options, I will say that the most successful of them are the ones that add margin to both parts and labor.
Think about what your risk exposures are, your tolerance for for loss or cost overruns in both parts and labor, and make your decision based on your own unique business environment.
Lets say, for example, you bid parts at cost and those costs unexpected rise because the manufacturer loses a key parts supplier and has to significantly raise prices to cover their new costs. If you didn't have a margin in your device pricing, you could potentially eat the full cost of that price increase as a loss rather than having it erode a profit margin. Or let's say that labor rates unexpectedly increase over the course of the project. If you were not pricing your labor with at least some level of margin, again you would face a loss rather than lower profit.
These are highly simplified examples, and I have no idea what your business model is, what your tolerance for absorbing unexpected costs are, or any number of other factors. Make the decision that best fits your long-term business strategy and goals. If you don't know what those are, then that is a whole other set of issues you should resolve before knowing what pricing structure is best for the health of your company.