It depends. If you cast your commander from the command zone, then yes, you still have to pay the so-called "commander tax", regardless of whether you cast that commander as a creature spell, a planeswalker spell, an Aura spell, or as something else (C.R. 903.3, 205.1a, 903.8, 118.9d, 118.9, 702.102a; see also this thread). However, if you cast your commander from anywhere else, the "commander tax" doesn't apply (C.R. 903.8; see also this thread).
Note, however, that the bestow cost for Kestia is 3GWU, no matter how often you've cast your commander this game (C.R. 702.1a). This is paid rather than the mana cost, but this doesn't change whether additional costs such as the "commander tax" have to be paid for that spell (C.R. 702.102a, 903.8, 118.9, 118.9d). Thus, in general, if Kestia is your commander and you cast it from the command zone for the second time this game, you have to pay either 5GWU (applying bestow) or 3GWU (not applying bestow), where the "commander tax" (here, 2) is included in each cost just given (C.R. 702.102a, 601.2f, 903.8).
Like, if she's died a few times does the bestow cost increase?
Note, however, that the bestow cost for Kestia is 3GWU, no matter how often you've cast your commander this game (C.R. 702.1a). This is paid rather than the mana cost, but this doesn't change whether additional costs such as the "commander tax" have to be paid for that spell (C.R. 702.102a, 903.8, 118.9, 118.9d). Thus, in general, if Kestia is your commander and you cast it from the command zone for the second time this game, you have to pay either 5GWU (applying bestow) or 3GWU (not applying bestow), where the "commander tax" (here, 2) is included in each cost just given (C.R. 702.102a, 601.2f, 903.8).
EDIT (Feb. 19): Clarification.