The Fibonacci sum $\sum_{n=0}^\infty \frac{1}{F_{2^n}}$ generalized

Your conjecture is indeed right. Before proving your conjecture, let us obtain an intermediate result first. Let us prove the following claim first.

CLAIM:

If we have a sequence given by the recurrence, $$a_{n+2} = ba_{n+1} + a_n,$$ with $a_0 =0 $ and $a_1 = 1$, we then have $$\boxed{\color{blue}{\displaystyle \sum_{k=0}^{N} \dfrac1{a_{2^k}} = 1 + \dfrac2b - \dfrac{a_{2^N-1}}{a_{2^N}}}}$$

Proof: Let us write out a few terms of this sequence, we get $$a_0 = 0, a_1 = 1, a_2 = b, a_3 = b^2 + 1, a_4 = b^3 + 2b, \cdots$$ The proof is by induction on $N$. For $N=1$, we have the left hand side to be $$\dfrac1{a_1} + \dfrac1{a_2} = 1 + \dfrac1b$$ while the right hand side is $$1 + \dfrac2b - \dfrac{a_1}{a_2} = 1 + \dfrac2b - \dfrac1{b} = 1 + \dfrac1b$$ For $N=2$, we have the left hand side to be $$\dfrac1{a_1} + \dfrac1{a_2} + \dfrac1{a_4} = 1 + \dfrac1b + \dfrac1{b^3 + 2b}$$ while the right hand side is $$1 + \dfrac2b - \dfrac{a_3}{a_4} = 1 + \dfrac2b - \dfrac{b^2+1}{b^3+2b} = 1 + \dfrac1b + \dfrac1b - \dfrac{b^2+1}{b^3+2b} = 1 + \dfrac1b + \dfrac1{b^3+2b}$$ Hence, it holds for $N=1$ and $N=2$. Now lets go ahead with induction now. Assume the result is true for $N=m$ i.e. we have $$\sum_{k=0}^{m} \dfrac1{a_{2^k}} = 1 + \dfrac2b - \dfrac{a_{2^m-1}}{a_{2^m}}$$ Now $$\sum_{k=0}^{m+1} \dfrac1{a_{2^k}} = 1 + \dfrac2b - \dfrac{a_{2^m-1}}{a_{2^m}} + \dfrac1{a_{2^{m+1}}}$$ Hence, we want to show that $$ - \dfrac{a_{2^m-1}}{a_{2^m}} + \dfrac1{a_{2^{m+1}}} = -\dfrac{a_{2^{m+1}-1}}{a_{2^{m+1}}}$$ i.e. $$\dfrac1{a_{2^{m+1}}} + \dfrac{a_{2^{m+1}-1}}{a_{2^{m+1}}} = \dfrac{a_{2^m-1}}{a_{2^m}}$$ i.e. $$a_{2^m}(1+a_{2^{m+1}-1}) = a_{2^m-1} a_{2^{m+1}} \,\,\,\, (\star)$$ which can be verified using the recurrence. In fact $(\dagger)$, a slightly more general version of $(\star)$, which is easier to check is true. $$a_{2k}(1+a_{4k-1}) = a_{2k-1} a_{4k} \,\,\,\, (\dagger)$$ i.e. $$a_{2k-1} a_{4k} - a_{2k} a_{4k-1} = a_{2k} \,\,\,\, (\dagger)$$ Hence, we get that $$\boxed{\color{red}{\displaystyle \sum_{k=0}^{N} \dfrac1{a_{2^k}} = 1 + \dfrac2b - \dfrac{a_{2^N-1}}{a_{2^N}}}}$$

Now letting $N \to \infty$, we see that your conjecture is indeed right. This is so since from the recurrence we get that $$\dfrac{a_{n+2}}{a_{n+1}} = b + \dfrac{a_n}{a_{n+1}}$$ If we have $\displaystyle \lim_{n \to \infty} \dfrac{a_n}{a_{n+1}} = L$, then we get that $$\dfrac1L = b + L$$ and since $L>0$, we have $L = \dfrac{\sqrt{b^2+4}-b}2$. Hence, $$\boxed{\color{red}{\displaystyle \sum_{k=0}^{\infty} \dfrac1{a_{2^k}} = \lim_{N \to \infty} \displaystyle \sum_{k=0}^{N} \dfrac1{a_{2^k}} = 1 + \dfrac2b - \lim_{N \to \infty} \dfrac{a_{2^N-1}}{a_{2^N}} = 1 + \dfrac2b - L = 1 + \dfrac2b + \dfrac{b}2 -\dfrac{\sqrt{b^2+4}}2}}$$

EDIT

After some googling, I found out that a similar result is true for a more general class of recurrences of the form $$a_{n+1} = P a_n + Q a_{n-1}$$ See this article for more details.

Also, try googling Millin series for more details.