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For example, if I am stating my character's thoughts in this way:
That was scary! He thought.
Can I switch to saying something like the below further on in my story?
He thought it was scary.
Or should I maintain consistency by using only one of the two methods throughout the entire manuscript? It's just that while writing, I felt using only one method seemed a bit redundant but I don't know if I'll lose consistency by alternating between the two.
The job of the writer is to provide something of value to the reader. And it is the reader that decides what is valuable and what is not. The advice here and elsewhere about writing is based upon general experiences with a population of readers. Thus, the writer should vary the length of sentences, show rather than tell, and, perhaps most importantly of all, break from expected conventions only when the writer thinks that the violation will provide enough value to pay back the additional cognitive cost to the reader of parsing the strangeness.
So the question is, what value does it provide (to the reader) if the writing switches between these two more-or-less equivalent modes of expression. Readers, particularly ones who consume a lot of material, are adept at picking up on conventions. While a reader might not stop and exclaim "Why?" when the convention changes, a little part of their brain will certainly wonder why. The writer had better have a good reason to disturb the flow the writing.
One reason that you might want to do this is to control how close the narrative is to the protagonist. Compare "Joe was cold and miserable" to "Joe shivered as the snow worked its way into his boots and chilled his hands." The boots-and-hand version brings the reader closer to the action. In a similar vein, the italics version brings the reader closer to the thinker. Throw in some physical reactions as the thinker thinks, and you can have the reader eyeball-to-eyeball with the protagonist.
But, what ever you chose to do, you need to think through the reasons for making those choices. Most quality writing involves such analysis. Often the writer has to experiment by writing a scene several different ways to see what achieves the desired effects better.
The answers in this forum cannot make these choices. All that these answers can do is provide some of the framework for making informed choices.
Firstly, I'd just drop the italics completely and rid myself of the whole problem.
They work poorly for foreign words and I think they don't add much when dealing with thoughts either. If I had to, I'd do some variant of:
That was scary, he thought.
I.e. no italics at all...
The two sentences you present are different in more ways than just italics. They also represent deep POV (the first version) and not so deep POV...
Think of it like this:
A: What did C think?
B: He thought it was scary.
A lot of distance.
Only add a "he"/"she"/"they" thought if you have scenes where you're showing several different character's thoughts in the same scene.
Think of it like dialog. If you can get away without a "they said", you do it. The same goes for thoughts (i.e. if only one person is thinking at the same time, you don't need to say who's thinking...)
I.e. do something like:
It was scary!
Now you're closer to the scared character and you're not reminded that it's a he and he's thinking. It just happens.
And finally, a "bonus":
A nit-picking reader might classify "That was scary!" as telling.
I'd recommend Margie Lawson's course "Empowering Characters' Emotions" as an introduction to writing more viscerally. For instance:
His mouth was dry, his palms were cold and wet and his heart was pounding so hard he felt it in his sternum. "You're not funny, put the gun down!"
