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Apologies for the super noob question but I was unsure as to whether this matters or not. My intercessor sergeant has a power sword and a pistol in each hand, and no bolt rifle visible. If I am to play in games will that mean he is classed as having the bolt rifle like the rest of the squad or will I need to make everything visible on the model somehow?

That is up to your gaming group. It is "correct" to have all a models optional wargear properly showing on the model so that there is no confusion for your opponent. In the case of an Intercessor Sergeant, it is a legal option to have Bolt Pistol and Power Sword with no Bolt Rifle. It would therefore be best to get a Bolt Rifle on that model in some way. Could be slung over a shoulder or even just on the base. Then there is no space for confusion on your opponent's part.

The RAW does not cover it.

So talk with your group and see what they say.

An intercessor sergeant with only a bolt pistol and no other weapons visible on the model is as legal as an intercessor sergeant with everything modeled on it.

Some people will give others grief about a missing bolt pistol or bolter, but wont even know what lash whips look like. So model how you want as long as the Dataslate is correct, you are golden per RAW.

Great, thank you for the help guys!

To clarify, there are no explicit game rules for this. It is an etiquette thing rather than a rules thing.

As has been pointed out WYSWYG (What You See is What You Get) is not formally in the rules anymore, but still has some traction in groups as informal etiquette. And for something like the rifle on the sarge, where the game impact is going to be minuscule, most people won’t mind. If you are worried, just note him at the start of the game to let your opponent know. “This guy modeled with two pistols has the same rifle as the squad, and counts-as with the free chainsword for the extra CC attack” Most people will respond with a “Nice conversion on the sarge, OK” and move on. The Rule of Cool covers a lot of sins.

It’s a bigger deal when things don’t look like what you are getting. Like not modeling a power fist. Suddenly the unit that looks like it’s not going to be able to do much to hard targets is punching holes in tanks. That’s when people get salty about models not being WYSWYG.

Pretty much everything has been covered already, so to sum it up neatly:

Model what you like, check with your fellow players before the game starts, include the proper gear clearly on the units datasheet, and when in doubt, have on hand an extra of whatever weapons you might want the model to have and lay them on the base for quick and easy visual verification for your fellow players.