Does Virgin implemented FTTP suffer from higher latency when in a congested area like the HFC product?
It can do. Although VM's FTTP uses fibre optic, the communication is RFoG (Radio Frequency over Glass), so your signal is still RF, and still hits the same gear at the head end of the network (CMTS) in the same way as HFC. The only benefit of RFoG is that it's almost immune to RF noise ingress, but the problems of DOCSIS remain, and if there were capacity problems then the outcome would be the same whether HFC or VM FTTP.
As for what can you tell from the Omni boxes, if it's a rectangle about eight inches high by four across, that's HFC. If you're seeing an eight inch square box, that's RFoG. The reason they're different is that the fibre optic can't be safely bent to the radius available in the older rectangle boxes. A Google image search for Virgin Media Omnibox will show the various different designs.
Hub 5 or Hub 4, you'll get what they have available, and any promises by sales agents won't mean a thing. As a Gig1 customer you'd get priority for any available Hub 5s, but that means only so much. Do you really need that speed? There's no latency benefit in higher speeds, and unless you're really going to make use of the speeds, you may end up paying for 18 months for something which you make very low utilisation of.
On a newer Lightning build, then you'd hope that they built with sufficient capacity, and usually that's the case. So all I can say is give it a go, you've got a 14 day cooling off period if there are problems - and presumably you'd have a BQM setup as soon as you go live. Also worth checking what your Openreach BQM is like - you complain about speeds, if this is for gaming then speed means nothing (as your comments suggest you already know). Some discussion around VM customer BQMs in this thread. Also be aware that VM's customer service is now worse than ever before - read a few pages of Trustpilot reviews to get a feel and set expectations.