First some generalizations:
1. Toslink optical S/PDIF output is often slightly inferior to Coaxial electrical S/PDIF output because the extra conversion stages that the clock signal has to pass through can add jitter (electrical to optical conversion at the transmitting end and optical to electrical conversion at the receiving end). Conversely, if the circuit or it's power supply is poorly designed, the Toslink connection can eliminate noise that the the Coaxial connection might be susceptible to.
2. Wireless transmission of a digital data stream can also isolate electrical noise that may be present at the source, but the wireless receiving device may also add jitter depending on it's design and implementation.
The newer Airport Express wireless N version (A1264) is known to have much higher jitter than the older wireless G version (A1084), and has caused problems with some DACs that use the ESS Sabre chips (and maybe some other DAC/Receiver chips?). One manufacturer who uses the ESS Sabre DAC chip, Peachtree Audio, has now even incorporated a switch to increase the "jitter aperture" so that it will work with the Airport Express N version.
In my own experience, I preferred the sound from a Toslink cable direct from my soundcard versus the Toslink cable from the Airport Express N. I still use the Airport Express N units, but for secondary casual listening systems and not my main system.
The Airport Express will also limit you to 16bit/48KHz output which may not be a limitation for you, but if you either have or plan to add higher resolution files to your library, the direct Toslink connection will reliably allow the native transmission of up to 24bit/96KHz files.
The actual synergy and sound quality will have a lot to do with the particular DAC that you use, and others may have realized perfectly good sound quality with the Airport Express or Apple TV. I am just relating my own observations of the Airport Express N Toslink output to my Rotel receiver DAC, the MHDT Paradisea DAC and the Stello D100 Signature DAC versus direct Toslink connection.
If you do decide to go with the Airport Express and don't currently own one, I would recommend finding an older wireless G (A1084) model with it's lower jitter, which can still be easily found on eBay and Craigslist.
Steve
