Hi Josco,
There is nothing special about Altera device packages that would preclude them from being tape and reeled. Whether a device is provided in a tray or on a reel has no bearing whatsoever on reliability, providing they are handled and stored correctly.
Altera's decision to provide devices in tray format is the easiest, safest and most cost effective path for them (this is the 'good' reason). There are just too many options and logistical concerns when devices are T&R'ed, though reliability by applying the T&R process itself is not one of them. Many customers use both Arrow and third party companies to T&R Altera products without issue.
Hopefully this helps to dispell your fears - if not, please elaborate on what your specific concerns are.
Stephen