Theory:

I know that there isn’t really a ghost,
My brother tells lies to keep the shed for his den;
There isn’t anyone staring or making strange noises
And the spider has been gone from his web
since I don’t know when,
I’ll go into that shed one day soon,

But not just yet...
Explanation:
 
As seen in the previous stanzas, the speaker had the desire to visit the shed. However, he had certain misgivings; the spider's web, the door that creaks, the feeling that someone staring through the cracked window, the possibility of a ghost hiding under the floorboards had frightened the speaker.
 
So, we see that the speaker is now trying to disregard the misgivings he had in the previous stanzas. For instance, he starts the fourth stanza by saying that there is no ghost hiding in the shed. He believes that his brother is trying to trick him into believing that there is a ghost as the latter considers the shed as his secret hideout. Hence, the brother cooked up the story of a ghost to prevent the speaker from going into the shed.

The speaker also tries to dismiss his other fears by claiming that no one is staring at him through the windows, nor is anyone making strange noises. In the first stanza, we saw how the speaker had described the noise from the shed. Though common sense told the speaker that the noise was from the rusty hinges, his misgivings would have probably let him imagine that the noise was made by "someone" rather than the doors. He then speaks about the spider's web that was hanging across the door. There was nothing to be afraid of as there were no spiders there. The spider has left the place and what remains is its harmless cobwebs.

When speaking of the spider, the speaker knows that it is long gone, but he isn't sure when it had left the place. The line "And the spider has been gone from his web since I don’t know when" reveals two aspects of the speaker's mind: for one, the speaker is sure that the spider had left its web but doesn't know when it happened. On the other hand, the line "since I don’t know when" can also suggest that the speaker isn't convinced by the thought that the spider has left the spot.

By dismissing his fears and doubts, the speaker indeed desires to check out the shed, at least for once. Again, the poet concludes the stanza with the modified refrain. He can be seen convincing himself that 'he would "go" into the shed one day soon'.

Speaking of the refrain, we had observed how the speaker's conviction of visiting the shed had transformed. In the first stanza, the speaker wanted to 'open the door'. Later, he assured himself that he would 'peep through the window'. In the third stanza, we see how the speaker had wanted to 'take a peek' at the shed. The transition is clear; the speaker gave into his doubts and fear and became less confident as the poem progressed. However, there comes a shift in the fourth stanza. He declares that he would "go into that shed one day soon". However, he adds a comma to the refrain and takes his thought further into the fifth stanza.

The short single-line fifth stanza further intensifies the transition of thoughts in the poem. Followed by the refrain from the previous stanza, the speaker says, "But not just yet...". Though the speaker was determined to go into the shed sometime soon, he wasn't ready for the adventure yet. The line reveals that the speaker is affected by the fears, and though he dreams of going into the shed, he couldn't persuade himself to do so. So, he would go, but only when he feels that he is ready to venture in.

Moreover, the stanza ends with 'three dots', formally known as 'ellipsis'. The three dots may imply several meanings. They may suggest 'uncertainty' as the speaker is unconvinced that he would visit the shed anytime soon. Or the dots may indicate hesitation of thought, as the speaker doesn't want to establish whether he would or could go into the shed. Either way, it is understood that the speaker is certain that he is not prepared to visit the shed anytime soon.

shed-166529_1920.jpg
The speaker is both curious and scared of the shed
  
Meanings of difficult words from the explanation:
 
S.No
Words
Meanings
1
MisgivingsA feeling of doubt or apprehension about the outcome or consequences of something
2
Hideout / Den
A room or secret place where a person can go to relax or be private
Reference:
National Council of Educational Research and Training (2007). Honeycomb. The Shed: Frank Flynn (pp. 48 -49). Published at the Publication Division by the Secretary, National Council of Educational Research and Training, Sri Aurobindo Marg, New Delhi.