If $L_1,L_2\in \mathrm{NP}$ and $w\in L_1$ or $w\in L_2$ then can $L_1\cup L_2=L$'s verifier use the same certificate $c$ for $w$?
Assume that $c_1$ and and $c_2$ are polynomial size certificates for $x \in V_1$ and $x \in V_2$. Then define $c=c_1\#c_2$, a new certificate formed by concatenation of $c_1$ and $c_2$ which is clearly polynomial size. Then $V_1$ and $V_2$ still can use $c$ as a certificate to verify $x\in V_1$ and $x\in V_2$. $V_1$ will use the left part of $c$ and the $V_2$ will use the right part of $c$. 


  Is a verifier by definition is deterministic TM?


Yes, the verifier is a deterministic TM, by definition.


  In the above answer, does $V_3$ runs $x,c$ on both $V_1$ and $V_2$ in the worst case?


You can treat $V_3$ as a TM which invokes (as subroutines) $V_1(x,c)$ and $V_2(x,c)$, so if $V_1$'s worst case is $O(f)$ and $V_2$'s worst case is $O(g)$ then $V_3$'s worst case is either $O(f)$ or $O(g)$ which is polynomial.