Buy both if price is right
A friend of mine has a Denon 989 that I will be buying from him. He also has a Harmon Kardon Pa5800 Pre power amp. I am not fully sure on whether I should take the amp too or just use the 989 . . .
Best option is to by both if the price is right. Both units put out just about the same power (HK is 80W/ch and the Denon is 115W/ch).
Keep in mind to double the sound output (+3 dB) from the HK would take doubling the watts (i.e ~160W). As a result, an 80W/ch or a 115W/ch amplifier have essentially the same capability.
So why buy both? The Denon's "advertised" power is measured when driving 2 channels. As you increase the number of channels the Denon is driving, it will have somewhat less power/ch available in each channel. Therefore, by adding the HK amp, you can divide the load between the two units (and power supplies) and increase each unit's ability to provide clean, undistorted sound to the speakers it is driving.
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Third possible options is: All of my speakers, minus the RC-Rs, can be bi-amped. Would I benefit to use the HK amp to power the lows and still use the denon outputs for the highs in each tower and center?
Yes and No. If you buy the HK, bi-amping is an option--but you will
NOT want to split each speaker's low/hi into the two separate amplification units (HK & Denon)!!

Also, bi-amping the Center with this set-up will be problematic. If you need a more detailed explanation, it can be provided later.
A more workable plan would be to use the Denon's "assignable amps" to bi-amp just the Front L/R speakers and then divide the overall number of amplified channels somewhat equally between the Denon and HK units.
For example, beside the bi-amped Front L/R also run the Center speaker from the Denon for a total of 5 "active" Denon amps; i.e. 2 for Front/L (bi-amped), 2 for Front/R (bi-am,ped) and 1 for the Center.
Then power the Surround L/R and Surround Back L/R speakers from the HK for a total of 4 "active" HK amps.
If you choose to bi-amp the Front L/R, then your Surround Back L/R speakers will have to be powered by the HK. This is done by connecting the Denon preamp outputs (labeled "Pre Out, SBL and SBR" on the receiver) to two of the HK inputs.
FWIW: Bi-amping will probably not make any noticable difference in the sound, but try it if you like, it will not hurt anything either.
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I know that Bi-amping is a normal thing, but can it be done with such different devices?
Not in the way you proposed above.
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Seems like such a waste to simply not use all of the outputs on the Denon.
Not really. The less channels (amps) each unit (HK or Denon) is driving will actually increase the power available to the channels you are using.
Cheers,
XEagleDriver