My Rogue trader player wants to hire some personal guards, looking at the requisition and crew quality/bfk troop quality what would be the best way to go about this, what starting stat line should I look at and how should I improve on those to represent higher trained bodyguards?

Use the Crew Quality value for relevant statistics - so a Competent (30) bodyguard has values of 30 in all Characteristics. It's dirt simply and works if you don't have the time to stat out better values. OTOH, a little work can produce much better results.

Do be aware that Veteran (50) and Elite (60) troops made this way are going to be really over-the-top and likely to seem rather unbalanced.

First, we've always just assumed that you already have "hirelings" or "bodyguards" simply by the fact that you have a ship full of soldiers to throw around as you'd wish, but, more to the point;

Second; while houseguards and various onboard personnell is mentioned over and over again in the books, I've yet to find any stats on it.  There are stats for "rival" Household Troops on pg.129 in Lure of the Expanse. You could use that.

If you as a GM want to specifically use individual "persons" for hirelings or real bodyguards that your Rogue Trader actually go out and find, I'd use the Household Troops as a sample and just randomize it a bit from that. Another alternative is to use the Minion rules in Black Crusade, if you've got access to that.

theres the faceless masses of crew and houseguards /voidsmen / random fighting man hired for the purposes of generic guard which is fine and easily abstracted with the crew rating although what i have tended to do is where a group of troops etc has been better trained -veteran elite etc then the relevant skills are increased to represent that so an armsman would have a BS of 60 for elite but the other skills stay at the original 30. but when shot they fall over and die without needing to track wounds etc.

Thats fine for large numbers of troops but when the rogue trader finds/handpicks and gets trained /implanted/equips a small group of utterly loyal bodyguards then the crew value kind of falls over as its too vague/abstract at that point.

I think i may have a look at the minion route. I know the player wont abuse the bodyguard and indeed it has caused several issues already because the bodyguard are utterly loyal to the trader and will not respond to anyone else if the trader has given them orders. (best quality volitor implants). i'm more than willing to kill the bodyguards off, but suspect that in character/npc terms because of the way the trader treats even the lowest born crew member there would be more than a few voluteers to replace losses (with long intervals for the training in their new duties etc)

We had a mercenary unit that my rogue trader hired - he got about 15 men + their equipment on a retainer simply by passing the acquisition check. They were largely controlled stats wise by the GM, but it was useful to be able to say "i station 3 of the mercs outside the cantina we are meeting the contacts in, and the other 12 in a truck parked round the corner".
I suppose if you want to have stats for them then avoid the crew rating suggestions for the reasons listed - too overpowered and abstract. Instead i'd suggest a base 30 in every attribute with each +5 boost to their combat attributes (Ws/Bs/S/T/Ag) increasing the rarity one step. I'd keep them simple with a flat 10 wounds however.