Is there any concern about a reduction of fluorescence intensity by epoxidation of Cyanine sequent double bonds during preparation and after the dye is released from nanoparticles in vivo? Does fluorescence intensity remain or get weak by epoxidation?

The pi system of Cyanines is electron deficient, so it will not epoxidate easily. Cyanines are not very stable to nucleophiles like alkali, but they can be exposed to electrophilic reagents without problems.

In water-based conditions, olefins are not epoxidized by water unless some special reagent like peroxide is added. The dyes get degraded or excreted from the organism with time, but there is a lot of time to do imaging before it.