If everyting comes from emptyness than what is energy

I have heard the logic system of Jains holds a logical category called "unfathomable".

adjective

1. not able to be fathomed, or completely understood; incomprehensible: heroism in the face of unfathomable conflict.
2. not able to be measured with a sounding line, or fathomed: unfathomable depths of the ocean.

Source: Dictionary.com

That means that transcendental phenomena are beyong the mind, uncomprehensable by the mind, unfathomable.

The Buddha did not say that 'everything' comes from 'nothing'. Specifically, the Buddha stated that Essential concepts - like 'Everything' and 'Nothing' are mere conceptual constructions, that the notion of independent entities, embodied by the term Self within his argument, are not evident within experience. It's not that everything comes from nothing, it's that neither everything nor nothing are evident as constructs.

This world, Kaccana, for the most part depends upon a duality—upon the notion of existence and the notion of nonexistence. But for one who sees the origin of the world as it really is with correct wisdom, there is no notion of nonexistence in regard to the world. And for one who sees the cessation of the world as it really is with correct wisdom, there is no notion of existence in regard to the world. SN 12.15

The above seems like a decent parallel to your question.

Madhyamaka tackles this issue in a more philosophical way though, look into Nagarjuna:

Neither from itself,
Nor from another,
Nor from both, nor without a cause,
Does anything, anywhere, whatsoever, arise.

Mulamadhyamakakarika

In addition, for energy specifically, Noether's theorem shows that energy is conserved, or more famously that:

Energy can neither be created nor destroyed, it can only change forms.

Emptiness with impermanence!

Buddha tells that everything originates from nothingness, emptiness, sunyata.

First, emptiness is not nothingness. Depending on the school of Tenets, emptiness refers to the absence of true existence, or to the absence of inherent existence, or to the absence of self-sufficient substantial existence, or to the absence of external establishment.

Second, emptiness cannot be a cause because a cause must preceed its effect, while emptiness and its basis (i.e. the object that is empty) arise, abide, cease simultaneously.

Third, emptiness cannot be a cause because emptiness is permanent and permanent phenomena do not perform a function.

The only context I know of where we find the expression, "phenomena arise from emptiness" is Tantra. In such a context, emptiness does not refer to emptiness itself, but to the mind realizing emptiness. This mind arises in this or that aspect.

How can something come from nothing.

It does not. Whatever is a product is produced by another [existent] phenomena.

Space, time and matter/energy is just and illusion.

Usually, we say that phenomena are "like an illusion", not that they are illusions. If you happen to read a traditional text that says that "phenomena are illusions", it means that they are "like an illusion." What we mean by this is that they do not exist the way they appear.

'Energy' is a word I never came across in any traditional text. However, we speak of 'matter' or 'form'. All objects that are apprehended by sense consciousnesses are 'matter'. This include smell, sound, taste, etc.

For a lucid, readable commentary on emptiness, take a look at Guy Newland's Introduction to Emptiness. Therein you will find a clarification of the difference between nothingness and dependent origination, which is another way of referring to emptiness. Jay Garfield's The Fundamental Wisdom of the Middle Way is an exceptional work and most germane when the question of sunyata arises. Another comprehensive tome on the subject is Jeffrey Hopkins' Meditation on Emptiness. Any one of these presentations will address your question as to the origin of illusion like everyday phenomena. On the topic of energy, it is humbling to recall Richard Feynman's remark, that "it is important in physics today to realize that we have no knowledge of what energy is". - https://en.m.wikiquote.org/wiki/Energy

Emptiness doesn't mean 'vacuum' or 'nothingness' (this view is refered to as nihilism sometimes in Buddhism). It means empty of self, or 'self-existence'.

In other words things are what they appear to be, and nothing else. The names you give to things, the thoughts, opinions you have about them, woven by your desires, fears, speculations etc. are transitory fabrications of your mind.

These fabrications are useful for remembering where you left your car keys, but become troublesome if you begin to believe in them as reality. So the Buddha reminds us that everything is in fact empty.