1) Not really, no. You can theoretically use the lowest level compression at build-time of the debs, but the Ubuntu builders don't do this. The slow part is probably not the decompression, but the unpacking of files and writing them to disk. Several things can affect disk I/O times here, including BIOS settings, drive rotational speed, and drive type. You could theoretically have the data archive inside the deb be data.tar though it would still have slight compression (or inflation), and wouldn't help with the speed of writing to disk.
2) See 1).
3) Yes, it would, if you were to take a binary deb and replace the data.tar.gz inside it, the size, timestamp, etc… would change. To be able to do something, you'd need to do it at build time of the deb package.
On the other hand, as I said, the speed issue is probably writing to disk. You can check your BIOS to change some settings for the disk. If your using a SATA disk, and your BIOS is set to communicate with it as IDE/ATAPI, then read/write speed is going to be extremely slow. Change the setting to AHCI if avaialble. Another common issue is disk RPM if you're not using an SSD. You didn't specify what size or RPM disk you are using, but a 2.5" 4500-5400 RPM disk is going to be slower than a 3.5" disk that does anywhere between 7200-15000 RPM. And a SATA I (1.5Gbps) disk is going to be slower than a SATA II (3.0 Gbps) or III (6.0 Gbps) disk. Disk cache size also plays an important role here. You also didn't say which Atom you had, or how much RAM, but they aren't as slow as one might think. They aren't a top shelf i7, but the amount of compression used in deb packages is not generally a problem for them.