Using ATI Catalyst drivers 9.10 with 6.10.17, I found out that the clocks of my 4870x2 go to 3D mode and stay there all the time BOINC Manager is running.

I'm not sure how you deduct that they "go to 3D mode". What program do you use for that?

This is happening without SETI having work to crunch on the GPU.
Is this normal?

As you've been told on Seti already, that project doesn't even have work for your GPU. When it has work (at this moment very little), it's for CPU and CUDA (or Nvidia) GPUs only. Not for ATI GPUs. And for the foreseeable future there won't be an ATI compatible app available from Seti either.

So if you only do Seti, or at least do no work for the projects that actually support ATI GPUs, there's no real use for you to allow BOINC to detect the GPU at this point. And really, simply said, that's all BOINC does: detect if a certain DLL file is present on your system and from that deduct that your ATI card is capable or not to do Brook+/CAL calculations on those projects that support it (Collatz and Milkyway). (If you want to see what it does in detail, read through Coproc.cpp)

And so, you can easily disable the GPU detection. To do so, make a file called cc_config.xml in your BOINC Data directory, or edit an existing one. The file doesn't come with BOINC, you will always have to make it yourself.

Add into it the following lines:

<cc_config>
    <options>
        <no_gpus>1</no_gpus>
    </options>
</cc_config> 

Save file, exit BOINC & restart it. A simple Advanced->Read config file won't do in this situation.