Would an object with mass traveling the speed of light destroy the whole universe because it would have infinite energy / mass?
If we understand the question as a limiting process, which is the only way it makes any sense, the answer is no. For illustrative simplicity, take a spherically symmetric isolated body, so that its exterior gravitational field is the Schwarzschild spacetime. Now boost this to ultrarelativistic speeds. In the speed of light limit, the result is a linearly polarized axisymmetric gravitational pp-wave, the Aichelburg-Sexl ultraboost.
Its effect on test particles it passes is an impulse: it instantaneously bends the worldlines, but does not destroy anything. You can think of this as infinite force acting for an infinitesimally small time, making the overall effect finite and nondestructive, somewhat analogously to a particle encountering a Dirac-delta potential in Newtonian physics.
This is similar to the ultrarelativistic limit of a moving electric charge. The electric field lines are Lorentz-contracted along the direction of travel, squeezing them together (image credit: wikipedia):
In the ultrarelativistic limit, the electric field in the transeverse direction becomes infinitely strong, but it is also Lorentz-contracted to be infinitely thin. Without ignoring the magnetic field, the result is an electromagnetic plane wave with a Dirac delta profile. The gravitational case is analogous, though quantitatively different. Some details on this can be found in arXiv:gr-qc/0110032.
My premise behind it possibly destroying the whole universe is that an object with infinite energy should also have infinite mass (E=mc^2, and infinity / c^2 is still infinity).
The concept of 'relativistic mass' is largely deprecated in modern physics. Mass is more properly related to energy and momentum via $(mc^2)^2 = E^2 - (pc)^2$.
One thought is that it could just form a black hole instead, ...
No, that's completely wrong. It doesn't become a black hole for the same reason it doesn't destroy the universe: the gravitating body moving relativistically past a stationary observer is physically equivalent to a relativistic observer moving past a stationary gravitating body. But the observer moving relativistically obviously does nothing to the gravitating body!