Hardboard should be damped down and allowed to dry fully before being laid otherwise it can expand and leave you with a floor like a mexican wave, as you've experienced. What floor covering are you planning on installing?
If carpet then you may be able to salvage the hardboard depending on how its been fixed down. If you can get it up relatively cleanly, damp it down, allow to dry then re-fit using divergent point staples and leave a 1mm gap between the edges.
As you paid someone to do the job they should come back and put it right but if they knew what they were doing the problem wouldn't have arisen.
Were they from a flooring company, general builders, chippy or handyman?
Unfortunately this highlights why each trade should stick to there own, but this doesn't mean that you won't get the problem even from people that are meant to know what they are doing, its pot luck sometimes unless you can get someone recommended or pay a premium price to a shop.
Good luck with whatever you try, but I'd be trying my hardest to get the installers back to put it right and if they refuse try a visit to citizens advice bureau, but if you paid them cash it will be your word against theirs.
I've just looked at your photos again - does the hardboard move up and down in areas where it looks like there are bubbles and can you hear "contact" with the boards underneath?
Some of the shapes are very regular which makes me think the hardboard is just following the shape of the floorboards and hardboard is too flexible to give you a completely smooth surface if your boards are very uneven.
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