Will the installation of the 2.04 client on the 10.9.5 mac affect the functioning of the 1.9.8 wallet, if I just leave the 1.9.8 wallet on the 10.6.8 system as is? I wouldn't expect so, but just to be sure.
That's perfectly fine, even if you use the same wallets (created from the same seeds) on both systems.
Finally, once the installation on the 10.9.5 system is completed and confirmed, is there any point of keeping the 1.9.8 wallet?
nerioseole alluded to one above—Electrum 2.x uses a different wallet format. If you give it a 1.9.8 wallet file, it will upgrade it to the new format behind the scenes (the seed remains the same). If you ever want to copy this 2.x wallet file to a machine that has Electrum 1.x on it, you'll need to instead either:
- Use a backup from Electrum 1.x, or
- simply restore from the seed.