As long as you have brand new original gaskets to install when the head is put back onto the block, i.e. cylinder head gasket, water pump gasket, valve cover gasket, intake/exhaust manifold gaskets as needed - and the head is torqued down and installed correctly - you should be fine. But these requirements aren't easy to fulfill.
Your engine may have tappets that require adjustment, or it may have hydraulic lifters based on how new it is. Ask Irshad if he knows which one your engine is, and precisely how the job will be done, why the head needs to be removed. Getting specific answers is important to making sure someone knows what they're doing.
Unfortunately, as an average end user, you're in a difficult spot where you need to verify the claims of mechanics before handing your expensive engine over to them. It's either this or live with the noise.
I'd wager he probably wants to remove the head so that he can determine the precise fit of the shims that need to be made for the valves to be adjusted correctly. He advised similarly for my 3ZZ-FE.
